Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

RESEARCH The Genexpress Index: A Resource for Discovery and the Genic Map of the R6mi Houlgatte, 1'2'3' R6gine Mariage-Samson, 1'2'3 Simone Duprat, 2 Anne Tessier, 2 Simone Bentolila, 1'2 Bernard Lamy, 2 and Charles Auffray 1'2'4

1Genexpress, Centre National de la Recherche Scientifique (CNRS) UPR420, 94801 Villejuif CEDEX, France; 2Genexpress, G4n6thon, 91002 Evry CEDEX, France

Detailed analysis of a set of 18,698 sequences derived from both ends of 10,979 human skeletal muscle and brain cDNA clones defined 6676 functional families, characterized by their sequence signatures over 5750 distinct human gene transcripts. About half of these have been assigned to specific utilizing 2733 eSTS markers, the polymerase chain reaction, and DNA from human-rodent somatic cell hybrids. Sequence and clone clustering and a functional classification together with comprehensive data base searches and annotations made it possible to develop extensive sequence and map cross-indexes, define electronic expression profiles, identify a new set of overlapping genes, and provide numerous new candidate genes for human pathologies.

During the last 20 years, since the first descrip- 1993; Park et al. 1993; Takeda et al. 1993; Affara tions of eucaryotic cDNA cloning (Rougeon et al. et al. 1994; Davies et al. 1994; Kerr et al. 1994; 1975; Efstratiadis et al. 1976), cDNA studies have Konishi et al. 1994; Kurata et al. 1994; Liew et al. played a central role in molecular genetics. Early 1994; Murakawa et al. 1994; Newman et al. 1994; attempts to systematically analyze gene tran- Nishiguchi et al. 1994; Nomura et al. 1994; Sasaki script repertoires were limited by available tech- et al. 1994; Soares et al. 1994; Sudo et al. 1994; nologies (Milner and Sutcliffe 1983; Putney et al. Auffray et al. 1995; Berry et al. 1995; Franco et al. 1983; Palazzolo et al. 1987; Sutcliffe 1988; Kato 1995; Frigerio et al. 1995; Pawlak et al. 1995). 1990), a situation that changed in the mid eight- This developing field has been recognized as an ies with the development of fluorescent-based important component of the Human Genome DNA sequencing (Smith et al. 1985, 1986). The Project for gene discovery (Collins and Galas initial proposal (Brenner 1990) and demonstra- 1993) and has been the subject of several reviews tions of the potential of systematic sequencing (Kato 1992; Southern 1992; Grausz and Auffray and mapping of cDNA clones (Adams et al. 1991; 1993; Matsubara and Okubo 1993; Sikela and H66g 1991; Hyde et al. 1991; Okubo et al. 1991; Auffray 1993). Mapping of the corresponding hu- Wilcox et al. 1991) were soon followed by numer- man genes has not developed as rapidly, al- ous medium- to large-scale cDNA sequencing though it is a limiting step in the identification of studies in a variety of tissues and species in both disease genes (for review, see Hochgeschwender animals and plants (Adams et al. 1992, 1993a,b; 1992; Parrish and Nelson 1993; Chen et al. 1994; Gieser and Swaroop 1992; Khan et al. 1992; Mc- Collins 1995). Thus, until recently, in addition to Combie et al. 1992; Okubo et al. 1992, 1994; the 3700 genes registered in the Genome Data Uchimiya et al. 1992, 1994; Waterston et al. Base, a relatively limited number of gene tran- 1992; H6fte et al. 1993; Matsubara and Okubo scripts characterized by cDNA sequencing have been assigned to a specific (Wilcox

3The first two authors contributed equally to this work. et al. 1991; Durkin et al. 1992; Gieser and Swa- 4Corresponing author. roop 1992; Khan et al. 1992; Polymeropoulos et E-MAIL [email protected]; FAX (33)(1)49 58 35 09. The complete data contained in Appendices 1 and 2 can be al. 1992, 1993; Fukushima et al. 1994; Murakawa found in electronic form at http://www.cshl.org/. et al. 1994; Berry et al. 1995).

272 ~I GENOME RESEARCH 5:272-304 ©1995 by Cold Spring Harbor Laboratory Press ISSN 1054-9803/95 $5.00 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

GENEXPRESS INDEX

We have recently reported the basic method- prefiltration and interactive validation steps, ology and primary results of our Integrated Mo- which provided links between sequences. Con- lecular Analysis of the human Genome and its tigs were defined as a set of sequences grouped Expression (IMAGE), a strategy to collect se- together by common links rather than multial- quence signatures from collections of cDNA ignments. This made it possible to group se- clones, quantitative hybridization signatures on quences that cannot be aligned such as alterna- high-density filters, and chromosomal assign- tively spliced sequences or sequences with low- ment of the corresponding genes using human- quality segments at their ends, when a third rodent somatic cell hybrids (Auffray et al. 1995). sequence was overlapping with both of them We collected 26,938 sequence signatures from (Fig. 1). This was also useful in the case of the both ends of cDNA clones from a human skeletal brain library, as some cDNA clones appeared to muscle and a normalized infant brain (Soares et be derived from unspliced mRNA. al. 1994) libraries and developed 2792 eSTS mark- A further advantage of this method is that ers (Auffray et al. 1995) that were assigned to spe- erroneous links based on repeats, composition cific chromosomes. In this paper we report a de- bias, or highly similar isogenes can be removed tailed description of the various steps of second- when detected at any stage, by inactivating it ary analyses of two-thirds of these sequences, and in the data base without any new calculation. most of the eSTS markers to index >5750 distinct Moreover, as in most cases we have obtained se- human gene transcripts by sequence clustering quences from both ends of the cDNA clones, it and data base comparison. We define electronic was possible to use clone links to group contigs expression profiles of the transcripts in the various tis- sues in which they have been 5' UTR CDS 3' UTR observed and the chromo- somal assignments of about mRNA half of the corresponding genes. We describe sequenc- ing and mapping cross- 5 indexes to facilitate the use of this resource for gene dis- covery, the construction of 2 the genic map of the human genome, and the identifica- 3 7 tion of disease genes.

4 8

SEQUENCE CLUSTERING 9 Each sequence was compared Figure 1 Sequence clustering strategy. Partial sequences (1-9) are repre- with all the others obtained sented by arrows, below the mRNA from which they were derived. Broken lines from the same library using indicate individual clones. Sequence analysis allowed us to find redundant the FASTA (Pearson 1990) sequences (>90% similar over their entire lengths) such as sequence 6 (iden- program. When a sequence tical to sequence 5) or 8 (identical to sequence 7). These redundant sequences had >90% similarity over its were not subject to further analysis. All nonredundant sequences were com- entire length with a previ- pared with each other to find overlapping sequences (sequences detected by ously registered sequence, it FASTA, with a Opt parameter >120, >90% identities, and validated by users) was considered redundant such as sequences 5 and 7, 2 and 3, 3 and 4. This allowed us to cluster sequences into contigs defined as sets of sequences linked either by redun- and its analysis was stopped. dancy or overlaps (sequences 1, 2-4, 5-8, 9) and to cluster together some Other sequences were con- sequences that could not be aligned (sequences 2 and 4) because of a low- sidered unique and were quality segment or alternative splicing (sequence 4 II), if a third sequence searched for more limited (sequence 3) overlapped with them. Sequences derived from the same clone overlaps by a second round were further clustered into Families (sequences 1-8, 9). After data base com- of comparisons. Both pro- parisons, families defined as Identical or Homolog to the same gene transcript cesses involved automatic were clustered together (sequences 1-9).

GENOME RESEARCH-ql1273 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

HOULGATTE El AL. together into families. When applied to the en- rules. For example, a complete but partial simi- tire set, the 18,698 sequences derived from larity with a nonhuman sequence can be more 10,979 cDNA clones were clustered into 12,713 significant than a limited but identical match contigs grouped in 6886 families. with a partial human sequence. This could be the case if the human gene has been partially se- quenced or if this sequence has been split in dif- ferent files, whereas the vertebrate homolog is DATA BASE COMPARISONS only defined as an mRNA stored in a unique file. All individual unique sequences were compared Therefore, if only the hit with the best score is with the GenBank nucleic acid sequences (Ben- taken into account, the identity with a known son et al. 1994), except the partial cDNA subsec- human sequence will not be detected. Similarly, tion and SWISS-PROT protein sequences (Bairoch the detection of 85% similarity with a vertebrate and Boeckmann 1994), using the BLAST (Alts- sequence could lead to classification of the se- chul et al. 1990; Gish and States 1993) family of quence as homologous, but this is erroneous if programs to define their level of similarity with the human homolog is already described and did known sequences. To avoid spurious similarities not produce a more significant match than with resulting from composition bias or repeats, we the vertebrate sequence. In that case, the query used a masked version of SWISS-PROT using the sequence is probably derived from a related gene, XNU (Claverie and States 1993) program. For nu- such as an isogene. For all these reasons, a sum- cleic acid comparisons, we first compared the se- mary of all informations collected including a quences with GenBank and a local repeat data summary of all the data base matches, FASTA base. Repeats detected with a high level of simi- alignment with their nucleic best matches, text larity were masked with the XBLAST (Claverie extraction of best-match files, six-frame transla- and States 1993) program, and all masked se- tion, coding frame prediction, nucleic acid, or quences were compared once again with Gen- protein motif predictions was provided to the us- Bank, to detect similarities that could have been ers for interpretation. underscored because of the presence of a repeat. A functional assignment was obtained in All sequences with no significant match most cases, but sometimes it was necessary to (P < 10 -s) in any data base were classified as Un- perform additional searches, such as multialign- known. To extend the initial matches detected by ments of sequences, data base searches with a BLAST, all the other sequences were unmasked limited part of the query sequence, or text and subjected to LFASTA alignment with their searches on data bases, in order to reach the final nucleic best matches. This was necessary because conclusion. The same functional assignment was insertions or deletions that are often present in derived for clones and families by gathering func- partial cDNA sequences are not taken into ac- tional assignment of their constitutive se- count by BLAST that provides only local uninter- quences. As different sequences could have sim- rupted alignments, whereas FASTA integrates the ilarities with different files of the nucleic acid presence of gaps. A direct FASTA search would data base derived from a single gene, it was nec- have overcome this problem, but an initial essary to create cross-indexes between these files. BLAST search directly provides a measurement of These cross-indexes were mainly derived from the statistical significance of the matches (Alts- SWISS-PROT cross-indexes, but many additionnal chul et al. 1994). links were derived by comparison of each nucleic Sequences were classified as Known if identi- acid sequence with the entire GenBank. These cal to a human sequence, Homolog if highly sim- cross-indexes link together different nucleic acid ilar to a vertebrate sequence, Related if having a sequences derived from a unique gene, but also partial similarity to a sequence of any species, the encoded protein, as well as the Genome Data Chimeric if having incoherent matches, or Un- Base (GDB) (Fasman et al. 1994) locus or On-line known if no match appeared significant. Se- Mendelian Inheritance in Man (OMIM) (Pearson quences from chimeric clones were not studied et al. 1994) entries. This also allowed us to estab- further. As correct classification depended on the lish a special category of link between sequences available informations of the hit sequences, such derived from the same gene but in different or- as position of the match or existence of multiple ganisms. The link of the nucleic acid sequences isogenes, we chose to favor human interpretation to SWISS-PROT files made it possible to access of all matches with basic principles and no strict annotations of much better quality than those

274 ~il GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

GENEXPRESS INDEX available in nucleic acid data bases which are able to the absence of the 3" end sequence (40% much more limited and sometimes erroneous. of the cases), alternative splicing (15%), alterna- On the other hand, as there are nucleic acid tive poly(A) site (33%), or internal priming of the sequences in GenBank that are not yet repre- mRNA (12%). Conversely, if 3' sequence is always sented as proteins in SWISS-PROT, this strategy obtained, gene transcript overestimation should probably failed to detect some matches, because have occured only in 4.3% of the cases. of differences in codon usage in different organ- Of the 6676 functional families, it can be isms. It will be possible to take them into account seen in Table I that 12.7% were already known in in the future using SWISS-PROT updates or by man, 3.2% are human homologs of a gene al- searching the GenPept nonredundant data base ready known in another vertebrate species, 7.6% that connects translation of nucleic acid data have a partial functional similarity with a known bases together with protein data base entries. gene, and 76.4% displayed no significant similar- Partial cDNA sequences were not searched ity. Overall, 2515 have been characterized inde- for sequence similarity in the initial process but pendently at least by partial sequencing. This were searched for overlapping segments as in the also indicates that of the 5823 new gene tran- clustering process. Tissue origin of the library was scripts described in this study, >4000 are de- extracted to define electronic expression profiles. scribed for the first time.

TRANSCRIPT ASSIGNMENT COMPARISON BETWEEN SKELETAL MUSCLE AND BRAIN LIBRARIES The cross-indexes allowed us to group different families classified as identical or homologous to Some differences between the muscle and brain the same gene that had not been clustered to- libraries can be observed when comparing the gether by their sequence similarities (Fig. 1). The most frequently represented gene transcripts (Ta- pool of 1276 such families was reduced by 210 ble 2). In the muscle library, the 10 most redun- (16.5%) during this process, leading to a total of dant transcripts are derived from already known 6676 functional families. This indicates that genes and represent -20% of the clones of this probably the number of families is an overesti- library. The most abundant previously uncharac- mation by -16.5% of the number of gene tran- terized transcript in man appears to be derived scripts characterized by partial sequencing. If this from a gene mapped to and re- coefficient is applied to all families, we can esti- lated to the Drosophila Kelch protein (rank 13). In mate that the 6886 families are probably repre- the brain library, the situation is completely dif- sentative of 5750 different human gene tran- ferent, as the most redundant transcript is the scripts. The situation appeared to be clearly dif- human homolog of rat neuronal olfactomedin- ferent in the muscle compared with the brain related protein localized in the endoplasmic re- library. In the muscle library, 24% of the known ticulum and mapped to chromosome 9 and the or homolog families were lost during the func- nine most abundant transcripts are derived from tional clustering step, whereas only 7% were lost four known, one homolog, and four unknown in the brain library. This discrepancy is mainly genes, which together represent only 1.4% of the attributable to the fact that, on average, 1.3 se- library. These differences are in part attributable quences are available for each clone in the mus- to variation in gene transcription in these tissues cle library (frequently, the 3' end sequence was but mostly to the normalization of the brain li- not obtained because of the difficulties of se- brary. This is also evident from the comparison quencing long poly(A) tails), whereas, on aver- between the functional classification of the dif- age, 1.8 sequences were available for each clone ferent clones or gene transcripts in the two librar- in the brain library that has relatively short ies (Table 3). In the muscle library, the most poly(A) tracts by cloning design (Soares et al. abundant transcripts encode cytoskeletal ele- 1994). This shows clearly that the gene transcript ments, metabolic proteins, or transport and stor- count can be largely overestimated when 3' end age proteins (functional redundancy of 6.31, sequences are not available, as is the case if only 3.40, and 3.48, respectively). In the brain library, 5' end sequencing is performed or if the cDNA the most abundant transcripts encode proteins library is random-primed. Failure to group to- involved in signaling, but global functional re- gether different families derived from the same dundancy is nearly identical for all the functional gene transcript in the brain library was attribut- classes (ranging from 1.49 to 2.19), and, there-

GENOME RESEARCH @ 275 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

HOULGATTE ET AL.

Table 1. Summary of the Similarity Classification (A) and Chromosomal Assignment (B) of the Gene Transcripts and Assessment of Mapping Accuracy (C)

cDNA partial sequences A Similiarity registered new total

Identical 438 415 853 Homologous 104 112 216 Related 165 342 507 Unknown 1393 3707 5100 Total 2100 4576 6676 Gene transcript mapping B Similarity G DB eSTS not tested total

Identical 481 101 271 853 Homologous 1 72 143 216 Related 3 180 324 507 Unknown 24 1919 3157 5100 Total 509 2272 3895 6676 eSTS markers

C identical partial different

GDB 124 (80%) 10 (6%) 22 (14%) Multiple 325 (86%) 20 (5%) 33 (9%)

(A) Comparison of individual sequences to nucleic acid (GenBank release 81.0 for muscle library, and release 84.0 for brain library) and protein (SWlSS-PROT) release 28) data bases allowed to classify each gene transcript as Identical, Homolog, Related or Unknown. Further comparison with the partial cDNA sequence data base subsection allowed detection of entries overlapping with any sequence of a registered gene transcript. Each family having at least one entry overlapping one of its constitutive sequences was considered as Registered, or New if not. (B) Each gene transcript having one eSTS derived from one of its partial sequences was considered as Assigned, or Known if identical to a human gene already mapped in GDB or GenBank. (C) Some known genes (156) already mapped in GDB were also assigned in this study (GDB), and 584 redundant eSTS allowing 323 pairwise comparisons (Multiple) were examined to assess the external and internal accuracy of the method. The different eSTS markers were defined as Identical if they produced the same result, Partial if they had one chromosome assignment in common, or Different.

fore, clone redundancy is no more a reflection of those obtained from the 3' end of the transcripts gene transcription. Another consequence of the and assigned to specific chromosomes using pan- normalization is that even though a large num- els of human-rodent somatic cell hybrids. Of the ber of sequences have already been obtained 2792 markers initially developed, most provided from brain libraries, additional sequencing of an unambiguous assignment, whereas 114 (3%) this normalized library will continue to yield a detected several chromosomes (Auffray et al. large proportion of new gene transcripts (as 1995). To assess the coherence of the assign- shown in Table 1A; discussed in Berry et al. ments, some eSTS markers were derived from 1995). known genes that had been localized previously, and in some cases, multiple eSTS markers were derived from different parts of the same tran- CHROMOSOMAL ASSIGNMENT script. Expressed sequence tagged site (eSTS) markers The sequence-clustering process described were derived from unique sequences, mainly above allowed us to map at the chromosomal

276 ~ll GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

GENEXPRESS INDEX

I 2

!- I o

° -i

i t

=i~'v..

I II II II II -~I II II~ II

' ...... = .... ~ ~ ~ ~!~;~ o iii iiii -i '! iiiii •- ~-~i!II ~~,~ =

w

~" u~:

li. m II In n." . ! -r ~.~i-- ~ ~ ~

m o" o' " ~ ~ o ,~ ",~ • ~o ~o~,~o~ ",~ • .~ • . # i ;~~~.'.~.-,~~ " ' ~:~ "~ ~i~ ~ ~ " ! I

GENOME RESEARCH ~l1277 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

HOULGATTE ET AL.

Table 3. Functional classification and global redundancy of all gene transcripts found in the muscle or brain libraries

A: Muscle Library

Clones Cytoskeleton Nucleic-Acid Pro'iein '" Recognition/' ' Signalling Transport/ Unclassified Tota/ Managing Managing Adhesion Storage 343 34 128 281 ...... 13 54 9'3:'.... 46 992 Homolosous ill El t:I ~1 FI ~1 ~1 II Related 56 29 23 24 2 191 6 35 194 Unknown ...... I 978 978 Total 410 77 169 330 16 86 108 1085 2281

Transcripts Cytoskeleton Nucleic-Acid [/roiein Metabolism Recognliion/ Signalling Transport/ Unclassified Total Managing Managing , Adhesion Storage Identical '" 33' 22 60 60 11 35 2~' ' 28 266 ...... l-iomolo~ous 5 8 13 21 i 9~ 5~ 12 74 Related ..... 27 19 21 16 2 13 6i . 19 123 Unknown 828 828 Total 65! 49 94 97 14 57 31 884 1291 , ,,,, ,

6-31 ..... 1.,:¥] 1 .:'IT] 3.,]i] 1.:~! 1.51 3.'~ ~] 1.77

B: Brain Library

Clones " cytoskeleton Nucleic-Acid Protein Metabolism Recognitionj Signalling Transport/ Unclassified Total Managing Managing Adhesion Storage •'ton ~t~ [0] I.~] [.~ l:ff, Ilt'J, '[:i~j :[.1 ',gll'J grp;I Homologous 17 22 35 33 6 76 38 99 326 Related '36 112 '82 69 32 108 30 161 630 Unknown 6419 6419 Total 153 ' 287 283 282 150 473 154 "'6916 8698

TranscripU Cytoskeleton Nucleic-Acid Proiein Metabolism Recognition/ Signalling Transport/ Unclassified Total Managing Managing Adhesion Storage I [dentical 41 100 81 96 50 150 41 133 692 Homologous' 8 16 16 22 4 36 23 38 163 Related 21 74 53 45 22 72 17 101 405 J,, , Unknown 4384 4384 Iota/ 7O 190 ' ' 150 163 76 258 81 4656 ' '5644 i ,i

1.51 1 ,.~ 1.~ ~ ~ ~ 1.,~ 1.541

Each individual gene transcript found in this study was classified using an arborescent functional classification based on the information of their best matches extracted from data bases. Main functional classes presented here are Cytoskeleton, Nucleic-Acid Managing (proteins involved in structure, repairing, replication or transcription of nucleic acids), Protein Managing (proteins involved in translation, maturation, targeting or degradation of proteins), Metabolism, Recognition and Adhesion (protein involved in cell or tissue adhesion, or recognition such as MHC), Signaling (proteins involved in intra- or extracellular signaling such as hormones or growth factors and their receptors, or proteins involved in second messenger pathways), Transport and Storage (proteins involved in chelation of inorganic compounds, transport across cell membranes, or polypeptide binding proteins), or Unclassified (protein with no known function, or new gene transcripts with no significant similarity). Functional classes are presented in terms of number of clones (Clones) or gene transcripts (Transcripts), and global functional redundancy (Redundancy) is defined as the number of clones divided by the number of gene transcripts for each functional class. Note that the sum of the gene transcripts in the two libraries is not equal to the total number of gene transcripts presented in this study, as some of them are found in both libraries.

level at least 2272 new genes using 2733 eSTS served for multiple assigments of the same tran- markers (Table 1B). In most of the cases (86%) script. The major causes of discrepancy appeared when the corresponding gene had already been to be the presence of an intron in the amplified mapped, these eSTS markers provided a localiza- sequences leading to the mapping of a related tion identical to that registered in GenBank or gene or pseudogene. This is clearly the case for GDB (Table 1C). A better correlation (91%) is ob- the human fructose biphosphate aldolase A gene

278 ~ GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

GENEXPRESS INDEX

-- =i 'i| i' _-- --" ~EE -- _= = _=_ .. _~ .= ,=,=,-- =_222 =-- ,= oEeo ~'6 ,_ = Eom E o! ~oo~ ~, "- oe _eee ~ o / O~i i,,~ 0 0 t- ~ i- E o e~ o6 i~m Ib (3 ~-- i.i: = -- c: ''~' I" ~I"" ~" I- ~') I~- "-- Q)! @ ill ~ "~l" ° ~ ~<,>,,>,-,<>-,- ,<.><.>~= ~

(3 , qj N ~i" Y ~" -- ~" ~" ~ E ~ ~" ~ I-- 0 N N < .~ ~, i~ ll.: c ~ ~i. = "~ :=.-.-.-'- zzz:~ :~ "~o o~ ~2 o 2~~ ~ ,-,

r,. i,.~ o~ o ,or,. = ~ r,. <-,

®®® 'i ® ® >~ >~'I'i ~ ~ ~ o o~ o, ~ - ~ ~ > >'>~>>'>'>>'>'~Z~ > > e- r" e- e.. ,..C e-' t-- ~,,,, e'," i-" e" e- ¢',, ¢- e- e,.i ?'. e" ¢-i,1~ I"

l 1'11 l"~ ell l'l~ I'~1 ,',-,'

I m I 1 I i 1 i -- I 1II i1 ~ 1 iI i I t~ I ~I , -- !1 i -- i J )t J J ~ I ~ J *1 *1 "i "1 "J "I "i "! "l *l "i "l "] "1 "1 "1 "1 "! "1 "1 *! "1 "i "1 "1 '1 " ~ ~ (.,) O r,,,) r,,.,) r,,,.) ¢,.) r,.) ~ ~ ~ O O r,,) ~ O ~ O r.,.) ¢,,,,) r,..) r,,,.) O r,,.) ¢,,) r,,)

I I'... I.-. ¢~,I~ oi (~I X ¢'xl itl I'.,, o

01 0: ol! Mc,n Pu_

fr" in' ~ rr iE ~ E II1 IZ! a3 I.l. r~ "i" r~ rn I13

¢"~! i ~ (~1 ~ ,,- ('%i i ("4 ~ ~ ii'%1 !liiitilllliiiiiIiiitiliii iiiiiiiiiiii itii,,'II iI0 o Ii

II

~l '~l' ,li' . l~l . i'll I~ ell

GENOME RESEARCH ill 279 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

HOULGATIE ET AL.

(ALDOA; GENX-3470), for which one eSTS mitochondrial form of this factor. The other pu- marker out of four correctly localized this gene tative overlapping genes are listed in Appendix on chromosome 16, whereas one mapped to 1F, including two of them that had already been chromosome 10, and the remaining two to chro- described (Ashworth 1993; Tsai et al. 1994). Some mosome 3 and 10, where the two aldolase A show a complex overlap and must be confirmed pseudogenes (ALDOAP1, ALDOAP2) are local- by direct genome sequencing and further de- ized. Conversely, the four eSTS markers derived tailed transcript analyses. from the slow binding protein C tran- The relatively important percentage (0.4%) script (GENX-3410) and the six derived from the of putative overlapping gene transcripts found in titin transcript (GENX-3338) always provided the this study suggests that the interaction between same correct result (chromosome 12 and chro- genes using common sequences for transcription mosome 2, respectively). or between mRNAs having complementary se- quences is an important mechanism for the reg- ulation of gene transcription. This may explain the conservation of some 3'-end untranslated re- GENE TRANSCRIPT OVERVIEW gions during evolution. This also suggests that a An overview of the characteristics of the 6676 higher percentage of genes may share a common gene transcripts described in this study is pro- overlapping segment with another gene and that vided in Appendix 1 (functional similarities) and the percentage observed here by partial sequenc- Appendix 2 (accession numbers and eSTS mark- ing could have been underestimated. ers). It should be clearly pointed out that posi- The main utility of the Genexpress Index is tional or functional informations have been ob- to provide new candidates for genes involved in tained in many instances from the analysis of human pathology with special reference to neu- different sequences derived from the same gene romuscular pathologies. Table 5A summarizes a transcript. As this set of sequences do not form in set of 56 genes (-6.5% of the known genes) that most cases a single contig from which a consen- have been characterized in this study and that sus can be derived, all information is gathered were already known to be defective in relation through links at this stage. with human pathologies. In addition, 17 other Some of the gene transcripts display signifi- transcripts display similarities with known defec- cant functional similarity with new putative tive genes (Table 5B) and could therefore repre- genes characterized by the systematic sequencing sent candidates for orphan pathologies. If a per- of different genomes (Table 4). This provides in- centage of 6.5% of defective genes is applied to dependent evidence that they are transcribed, at the whole set of genes described in this study, we least in man, and underlines the complementar- probably characterized more than 400 genes in- ity between genomic and partial cDNA sequenc- volved in human pathology. The utility of partial ing approaches. This also indicates the impor- cDNA sequencing for the identification of genes tance of the integration of data from different involved in neuromuscular diseases is underlined organisms, as many functional features can be by the fact that the recently cloned Survival Mo- derived from the complete sequence of a gene in tor Neuron gene (Lefebvre et al. 1995) involved another species. in spinal atrophy was registered early in this Another 27 gene transcripts are of particular study (GENX-4903). interest because they appear to be derived from overlapping complementary strands of common segments of the genome. Figure 2 shows the se- quence alignment of a gene transcript (GENX- CONCLUSIONS AND PERSPECTIVES 5024) overlapping with the human [3-hex- Partial sequencing of cDNA clones and chromo- osaminidase gene in their 3' regions. This gene somal assignment of the corresponding genes are transcript exhibits significant similarity with the preliminary steps in the identification of dis- G from Thermus aquaticus (Fig. ease genes and need to be integrated in a more 2B) as well as with that of yeast mitochondrial general way, including complete sequencing, elongation factor G (not available in data bases at precise mapping, and detailed expression, and the time of the initial search). The better similar- functional studies. This is the purpose of the IM- ity with this last sequence suggests that the AGE consortium in which laboratories of various GENX-5024 transcript may encode the human size and expertise collaborate worldwide to char-

280 ~il GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

GENEXPRESS INDEX

A) Figure 2 Overlapping genes. (A) Schematic rep- resentation of a gene transcript (GENX-5024) re- lated to T. aquaticus elongation factor G (P13551) P13551 and overlapping the human gene encoding [[3-hex- osaminidase (M23294). Partial cDNA sequences are shown as arrows, coding regions, or proteins as hatched boxes, 3'-untranslated regions as dotted boxes, and introns or genomic DNA as solid boxes. Broken lines indicate unsequenced parts of the F15189 F15209 cDNA clones. Accession numbers are above their 5.@ --~ AAA 3' representation. Note that this transcript overlaps by 25 bp with the 13- transcript (Gen- Bank M13519, not shown) and is identical to the M23294 untranscribed genomic DNA downstream of this gene. (B) Sequence alignments of the 5' end se- quence of GENX-5024 (lane 1) and its putative translation (lane 2) with T. aquaticus elongation fac- tor G. (C) Sequence alignments of the 3' end se- B) quence of GENX-5024 (F15209) with the genomic (M23294) and the mRNA (M13519) sequences of F15189 GGATGACTTATGTGCATTGGCATTTAAAGTTCTCCATGACAAGCAGCGAGG-CCACTGGT D D L C A L A F K V L H D K Q R G P L V the human 13-hexosaminidase gene. Poly(A) signals P13551 G P L A A L A F K I M A D P Y V G R L T are shown in boldface.

F15189 TTT-ATGCGCATT TACTCAGGCACTATAAAACCC CAGTTGGC CATTCATAATAT TAATGG X M R I Y S G T I K P Q L A I H N I N G P13551 F I R V Y S G T L T S G S Y V Y N T T K

F15189 AAACTGCACGGAGAGAATAAGTCGTCTGCTTTTGCCGTTTGCTGACCAACATGTAGAAAT N C T E R I S R L L L P F A D Q H V E I et al. 1995). The availability of the 2792 eSTS P13551 G R K E R V A R L L R M H A N H R E E V markers that we have developed (Auffray et al. F15189 CCCTTCATTGACTGCTGGTAACATTGCTTTGACTGTTGGG-TTAAACATACTGCCACTGG 1995), together with >1200 others developed by P S L T A G N I A L T V G X K H T A T G P13551 E E L K A G D L G A V V G L K E T I T G Dr. Polymeropoulos (Polymeropoulos et al. 1992, F15189 AGACACCATTGTCTCATCCAAGTCCAGTGCATTAGCTGCA 1993; M. Polymeropoulos, pets. comm.), provide D T I V S S K $ S A L A A P13551 D T L V G E D A P R V I L the opportunity to double the number of mapped genes and therefore enhance the proba- c) bility of identifying those involved in human pa- F15209 GAATAAAATATTTTTATTGATTGA-CCTTTGACCCTCTATCTTATTACATTT M23294 GAATAAAATATTTTTATTGATTGAACCTTTGACCCTCTATCTTATTACATTT thologies. 1413519 GAATAAAATATTTTTATTGATTGAA The value of this resource to complement the F15209 AGAGGCCTGGCATCTTTCTTGTGAGACAAGCTTAAGGACACAAAAGAAACAC M23294 AGAGGCCTGGCATCTTTCTTGTGAGACAAGCTTAAGGACACAAAAGAAACAC positional paradigm (Collins 1995) is exemplified

F15209 AACTTTGTGATACCACTCT-CTGAAGGCTACTTATAGTAATAACTTCATAGA by the process that led to the identification of the 1423294 AACTTTGTGATACCACTCTTCTGAAGGCTACTTATAGTAATAACTTCATAGA gene responsible for the recessive form of limb- F15209 TGA-CAGCATGATTCAGGTACAGTGGCTTTAAACATCAAAGCACATTTCTCA 1423294 TGAACAGCATGATTCAGGTACAGTGGCTTTAAACATCAAAGCACATTTCTCA girdle muscular dystrophy (Richard et al. 1994,

F15209 TTATATAAATT AAAACGGGTGGCTC CAGTGCCAC TATCAAAGCT TA 1995; Chiannikulchai et al. 1995). In monitoring M23294 TTATATAAATTAAA the progress of the genic map, toward the goal of 100-kb resolution (Cox et al. 1994), intervals of 50-250 Mb (chromosome), 10-50 Mb (cytoge- netic interval), 1-10 Mb (integrated genetic map), and <1 Mb (cloned and mapped DNA frag- acterize common ordered collections of cDNA ment) are important milestones. As it is esti- clones by a variety of complementary ap- mated that the human genome contains some proaches. This includes positioning of all the 60,000 to 80,000 genes (Antequera and Bird genes characterized in this study in the inte- 1993, 1994; Fields et al. 1994), the current genic grated genetic, cytogenetic, and physical maps of map is only -10% complete at the first level of the human genome using DNA fragments cloned chromosomal resolution. To contribute to the in yeast artificial chromosomes (YACs) and other progress toward a dense and comprehensive vectors and rearrangement, breakpoint, and radi- genic map, we are currently extending the set of ation reduced somatic cell hybrids (Cox et al. eSTS markers to the remaining indexed genes in 1990; Weissenbach et al. 1992; Cohen et al. 1993; collaboration with IMAGE consortium collabora- Gyapay et al. 1994; Walter et al. 1994; Chumakov tors. This has already allowed regional localiza-

GENOME RESEARCH@ 281 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

HOULGATTE ET AL.

O m o

@.

E

eII

I~. qq~. ~. ~ ~ ~...~!

1111111111111111l!lllliil lll ll ililllllllllllllll

® ~- ~

q,

<

282 @ GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

GENEXPRESS INDEX

gU i Jt B

i II IP

I! 5 III t IP

J

~1-, , ,11- iI1~ o sl,~l,~ ~/~

I!111 ixt~ i~1 I 1 I~1-1~

,,111~1111,,z 31 , illilllll ]lUll ittttttttttttttttf lllillllllltllllll m

GENOME RESEARCH @ 283 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

HOULGATTE ET AL. tion of eSTS markers assigned to several chromo- gram team and the staff at G~n~thon and CNRS somes at one to a few megabase resolution for their dedication and support. The IMAGE (Callen et al. 1995; Rosier et al. 1995; C. Auffray consortium is coordinated by C.A. in collabora- et al., unpubl.). tion with Dr. Greg Lennon at the Department of As a fraction of-15% of the eSTS markers also Energy Genome Center in Livermore, Dr. Mihae- amplify the corresponding genes in the mouse, it lis Polymeropoulos at the National Center for will be possible to use them directly to integrate Human Genome Research, National Institutes of the human and mouse maps. These markers are Health, Bethesda, and Dr. Bento Soares at Colum- also versatile tools that can be used in RT-PCR bia University, New York. The Genexpress Pro- experiments to monitor the expression profiles of gram is supported by Association Fransaise con- the transcripts in a large number of tissues, cell tre les Myopathies (AFM), CNRS, and grants from lines, and species in various physiological and the Ministbre de la Recherche et de l'Espace pathological situations. Cross-referencing with (MRE), Groupement de Recherches et d'Etudes de the results collected in the study of the genomes G~nomes (GREG), and the European Union of other model organisms will be instrumental in Biomed 1 Program to C.A. deciphering the functions of the large number of The publication costs of this article were de- new genes indexed in this study and other simi- frayed in part by payment of page charges. This lar programs. article must therefore be hereby marked "adver- tisement" in accordance with 18 USC section MATERIAL AND DATA AVAILABILITY 1734 solely to indicate this fact. The cDNA sequences have been registered to the EMBL Data Library, and the eSTS markers in GDB. The Genexpress index is available on the REFERENCES Internet by anonymous FTP at the address ftp.in- Adams, M.D., J.M. Kelley, J.D. Gocayne, M. Dubnick, fobiogen.fr in the/pub/db/Genexpress directory M.H. Polymeropoulos, H. Xiao, C.R. Merril, A. Wu, B. with the associated help file READ_ME. In addi- Olde, R.F. Moreno, A.R. Kerlavage, W.R. McCombie, and J.C. Venter. 1991. Complementary DNA sequencing: tion, they can be downloaded or consulted on Expressed sequence tags and Human Genome project. the Genome Research World Wide Web server at Science 252: 1651-1656. address http://www.cshl.org. Information on the IMAGE Consortium is available from Dr. Greg Adams, M.D., M. Dubnick, A.R. Kerlavage, R. Moreno, Lennon, Department of Energy Genome Center, J.M. Kelley, T.R. Utterback, J.W. Nagle, C. Fields, and J.C. Lawrence Livermore: http://www.bio.llnl.gov/ Venter. 1992. Sequence identification of 2,375 human brain genes. Nature 355: 632-635. bbrp/genome/genome.htlm; cDNA clones can be obtained from Dr. Hans Lerach, Reference Library Adams, M.D., A.R. Kerlavage, C. Fields, and J.C. Venter. Data Base, Max Planck Institute ffir Molekulare 1993a. 3,400 new expressed sequence tags identify Genetik, Berlin, Germany: http://gea.lif.icnet.uk/ diversity of transcripts in human brain. Nature Genet. and from Dr. Keith Gibson, Human Genome Pro- 4: 256-267. gram Resource Center, Hinxton, UK: http:// www.hgmp.mrc.uk/. Primer pairs will be avail- Adams, M.D., M.B. Soares, A.R. Kerlavage, C. Fields, and J.C. Venter. 1993b. Rapid cDNA sequencing (expressed able from Research Genetics. Other requests con- sequence tags) from a directionally cloned human infant cerning additional information and reagents brain cDNA library. Nature Genet. 4: 373-380. should be directed to the Email address: [email protected]. Affara, N.A., E. Bentley, P. Davey, A. Pelmear, and M.H. Jones. 1994. The identification of novel gene sequences NOTE ADDED IN PROOF of the human adult testis. Genomics 22: 205-210.

Adams et al. (1995. Nature 377: $3-$174) have Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. described an "Initial assessment of human gene Lipman. 1990. Basic local alignment search tool. J. Mol. diversity and expression patterns based on 83 mil- Biol. 215: 403-410. lion nucleotides of cDNA sequence" at the time this paper was accepted for publication. Altschul, S.F., M.S. Boguski, W. Gish, and J.C. Wooton. 1994. Issues in searching molecular sequence databases. ACKNOWLEDGMENTS Nature Genet. 6: 119-129. We thank all members of the Genexpress Pro- Antequera, F. and A. Bird. 1993. Number of CpG islands

284 ~il GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

GENEXPRESS INDEX and genes in human and mouse. Proc. Natl. Acad. Sci. Premiere g6n6ration de la carte physique du g6nome 90: 11995-11999. humain. C.R. Acad. Sci. Paris (Life Sciences) 316: 1484-1488. --. 1994. Predicting the total number of human genes. Nature Genet. 8: 114. Collins, F.S. 1995. Positional cloning moves from perditional to traditional. Nature Genet. 9' 347-350. Ashworth, A. 1993. Two acetyl-CoA acetyltransferase genes located in the t-complex region of the mouse Collins, F. and D. Galas. 1993. A new five-year plan for chromosome 17 partially overlap the Tcp-1 and Tcp-lx the US human genome project. Science 262: 43-46. genes. Genomics 18" 195-198. Cox, D.R., M. Burmeister, E.R. Price, S. Kim, and R.M. Auffray, C., B. B6har, F. Bois, C. Bouchier, C. Da Silva, Myers. 1990. Radiation hybrid mapping: A somatic cell M.-D. Devignes, S. Duprat, R. Houlgatte, M.-N. Jumeau, genetic method for constructing high resolution maps of B. Lamy, F. Lorenzo, H. Mitchell, R. Mariage-Samson, G. mammalian chromosomes. Science 250- 245-250. Pi~tu, Y. Pouliot, C. S~bastiani-Kabaktchis, and A. Tessier. 1995. IMAGE : Integrated Molecular Analysis of Cox, D.R., E.D. Green, E.S. Lander, D. Cohen, and R.M. the human Genome and its Expression. C.R. Acad. Sci. Myers. 1994. Assessing mapping progress in the human Paris (Life sciences) 318: 263-272. genome project. Science 265: 2031-2032.

Bairoch, A. and B. Boeckmann. 1994. The Swiss-Prot Davies, R.W., A.B. Roberts, A.J. Morris, G.W. Griffith, J. protein sequence data bank: Current status. Nucleic Acids Jerecic, s. Ghandi, K. Kaiser, and A. Savioz. 1994. Res. 22- 3578-3580. Enhanced access to rare brain cDNAs by prescreening libraries: 207 new mouse brain ESTs. Genomics Benson, D.A., M. Boguski, D.J. Lipman, and J. Ostell. 24" 456-463. 1994. GenBank. Nucleic Acids Res. 22- 3441-3444. Durkin, A.S., D.R. Maglott, and W.C. Nierman. 1992. Berry, R., T.J. Stevens, N.A.R. Walter, A.S. Wilcox, T. Chromosomal assignment of 38 human brain expressed Rubano, J.A. Hopkins, J. Weber, R. Goold, M.B. Soares, sequence tags (ESTs) by analyzing fluorescently labeled and J.M. Sikela. 1995. Gene-based sequence-tagged-sites PCR products from hybrid cell panels. Genomics (STSs) as the basis for a human gene map. Nature Genet. 14: 808-810. 10:415-423. Efstratiadis, A., F.C. Kafatos, A.M. Maxam, and T. Brenner, S. 1990. The human genome: The nature of the Maniatis. 1976. Enzymatic in vitro synthesis of globin enterprise. CIBA Found. Syrup. 149: 6-17. genes. Cell 7-279-288. Callen, D., S.A. Lane, H. Kozman, G. Kremmidiotis, S.A. Fasman, K.H., A.J. Cuticchia, and D.T. Kingsbury. 1994. Whitmore, M. Lowenstein, N.A. Doggett, N. Kenmochi, The GDB human genome database anno 1994. Nucleic D.C. Page, D.R. Maglott, W.C. Nierman, K. Murakawa, R. Acids Res. 22" 3462-3469. Berry, J.M. Sikela, R. Houlgatte, C. Auffray, and G.R. Sutherland. 1995. Integration of transcript and genetic maps of chromosome 16 at near 1 Mb resolution: Fields, C., M.D. Adams, O. White, and J.C. venter. 1994. Demonstration of a hot spot for recombination at How many genes in the human genome? Nature Genet. 16p12. Genomics 29: 503-511. 7: 345-346.

Chen, E., M. d'Urso, and D. Schlessinger. 1994. Franco, G.R., M.D. Adams, M.B. Soares, A.J. Simpson, Functional mapping of the human genome by cDNA J.C. venter, and S.D. Pena. 1995. Identification of new localization versus sequencing. BioEssays 16" 693-698. Schistosoma mansoni genes by the EST strategy using a directional cDNA library. Gene 152: 141-147. Chiannikulchai, N., P. Pasturaud, I. Richard, C. Auffray, and J. Beckmann. 1995. An expression map of the Frigerio, J.M., P. Berthezene, P. Garrido, E. Ortiz, S. chromosome 15q15 region, containing a gene for the Barthellemy, S. Vasseur, B. Sastre, I. Seleznieff, J.C. recessive form of limb-girdle muscular dystrophy, Dagorn, and J.L. Iovanna. 1995. Analysis of 2166 clones LGMD2A. Hum. Mol. Genet. 4: 717-725. from a human colorectal cancer cDNA library by partial sequencing. Hum. Mol. Genet. 4:37-43. Chumakov, I.M., P. Rigault, I. LeGall, C. Bellan~-Chantelot, A. Billault, S. Guillou, P. Soularue, G. Fukushima, A., K. Okubo, H. Sugino, N. Hori, R. Matoba, Guasconi, E. Poullier, I. Gross, et al. 1995. A YAC contig T. Niiyama, K. Murakawa, J. Yoshii, M. Yokoyama, and map of the human genome. Nature 377: $175-$297. K. Matsubara. 1994. Chromosomal assignment of HepG2 3'-directed partial cDNA sequences by Southern blot Claverie, J.-M. and D. States. 1993. Information hybridization using monochromosomal hybrid cell enhancement methods for large scale sequence analysis. panels. Genomics 22: 127-136. Comput. Chem. 17" 191-201. Gieser, L. and A. Swaroop. 1992. Expressed sequence tags Cohen, D., I. Chumakov, and J. Weissenbach. 1993. and chromosomal localization of cDNA clones from a

GENOME RESEARCH@ 285 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

HOULGATTE ET AL. subtracted retinal pigment epithelium library. Genomics Toyama, Y. Miyamato, T. Kirihara, K. Hayasaka, A. 13: 873-876. Miyao, L. Monna, H.S. Zhong, Y. Tamura, Z.X. Wang, T. Momma, Y. Umehara, M. Yano, T. Sasaki, and Y. Gish, W. and D.J. States. 1993. Identification of protein Minobe. 1994. A 300 kilobase interval genetic map of coding regions by database similarity search. Nature rice including 883 expressed sequences. Nature Genet. Genet. 3: 266-272. 8: 365-372.

Grausz, D. and C. Auffray. 1993. Strategies in cDNA Lefebvre, S., L. Bfirglen, S. Reboullet, O. Clermont, P. programs. Genomics 17: 530-532. Burlet, P. Viollet, B. B6nichou, C. Cruaud, P. Millasseau, M. Zeviani, D. Le Paslier, J. Fr~zal, D. Cohen, J. Gyapay, G., J. Morissette, A. Vignal, C. Dib, C. Fizames, Weissenbach, A. Munnich, and J. Melki. 1995. P. Millasseau, S. Marc, G. Bernardi, M. Lathrop, and J. Identification and characterization of a spinal muscular Weissenbach. 1994. The 1993-94 G~n6thon human atrophy-determining gene. Cell 80: 155-165. genetic linkage map. Nature Genet. 7: 246-339. Liew, C.C., D.M. Hwang, Y.W. Fung, C. Laurenssens, E. Hochgeschwender, V. 1992. Toward a transcriptional Cukerman, S. Tsui, and C.Y. Lee. 1994. A catalogue of map of the human genome. Trends Genet. 8: 41-44. genes in the cardiovascular system as identified by expressed sequence tags. Proc. Natl. Acad. Sci. H6fte, H., T. Desprez, J. Amselem, H. Chiapello, M. 91: 10645-10649. Caboche, A. Moisan, M.F. Jourjon, J.L. Charpenteau, P. Berthomieu, D. Guerrier, J. Giraudat, F. Quigley, F. Matsubara, K. and K. Okubo. 1993. Identification of new Thomas, D.Y. Yu, R. Mache, M. Raynal, R. Cooke, F. genes by systematic analysis of cDNAs and database Grellet, M. Delseny, Y. Parmentier, G. Marcillac, C. construction. Curr. Opin. Biotech. 4: 672-677. Gigot, J. Fleck, G. Philipps, M. Axelos, C. Bardet, D. Tremousaygue, and B. Lescure. 1993. An inventory of McCombie, W.R., M.D. Adams, J.M. Kelley, M.G. 1152 expressed sequence tags obtained by partial FitzGerarld, T.R. Utterback, M. Khan, M. Dubnick, A.R. sequencing of cDNAs from Arabidopsis thaliana. Plant J. Kerlavage, J.C. Venter, and C. Fields. 1992. 4: 1051-1061. Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. HOOg, C. 1991. Isolation of a large number of novel Nature Genet. 1: 124-131. mammalian genes by a differential cDNA library searching strategy. Nucleic Acids Res. 19: 6123-6127. Milner, R.J. and J.G. Sutcliffe. 1983. in rat brain. Nucleic Acids Res. 11: 5497-5517. Hyde, D.R., K.L. Mecklenburg, J.A. Pollock, T.S. Vihtelic, and S. Benzer. 1991. Twenty Drosophila visual system Murakawa, K., K. Matsubara, A. Fukushima, J. Yoshii, cDNA clones: One is homolog of human arrestin. Proc. and K. Okubo. 1994. Chromosomal assignments of Natl. Acad. Sci. 87: 1008-1012. 3'-directed partial cDNA sequences representing novel genes expressed in granulocytoid cells. Genomics Kato, K. 1990. A collection of cDNA clones with specific 23: 379-389. expression patterns in mouse brain. Eur. J. Neurosci. 2: 704-711. Newman, T., F.J. de Bruijn, P. Green, K. Keegstra, H. Kende, L. Mclntosh, J. Ohlrogge, N. Raikhel, S. --. 1992. Finding new genes in the nervous system Somerville, M. Thomashow, E. Retzel, and C. Somerville. by cDNA analysis. Trends Neurosci. 15: 319-323. 1994. Genes galore: A summary of methods for accessing results from the large-scale partial sequencing of Kerr, S.M., S. Vambrie, S.J. McKay, and H.J. Cooke. 1994. anonymous Arabidopsis cDNA clones. Plant Physiol. Analysis of cDNA sequences from mouse testis. 106: 1241-1255. Mammalian Genome 5: 557-565. Nishiguchi, S., T. Joh, K. Horie, Z. Zou, T. Yasunaga, and Khan, A.S., A.S. Wilcox, M.H. Polymeropoulos, J.A. K. Shimada. 1994. A survey of genes expressed in Hopkins, T.J. Stevens, M. Robinson, A.K. Orpana, and undifferentiated mouse embryonal carcinoma F9 cells: J.M. Sikela. 1992. Single pass sequencing and physical Characterization of low-abundance mRNAs. J. Biochem. and genetic mapping of human brain cDNAs. Nature 116" 128-139. Genet. 2: 180-185. Nomura, N., N. Miyajima, T. Sazuka, A. Tanaka, Y. Konishi, K., Y. Morishima, E. Ueda, Y. Kibe, K. Kawarahayasi, S. Sato, T. Nagase, N. Seki, K. Ishikawa, Nonomura, K. Yamanishi, and H. Yasuno. 1994. and S. Tabata. 1994. Prediction of the coding sequences Cataloguing of genes expressed in human keratinocytes: of unidentified human genes. 1. The coding sequences Analysis of 607 randomly isolated cDNA sequences. of 40 new genes (KIAAOOO1-KIAAO040) deduced by Biochem. Biophys. Res. Commun. 202: 976-983. analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1. DNA Res. 1: 27-35. Kurata, N., Y. Nagamura, K. Yamamoto, Y. Harushima, N. Sue, J. Wu, B.A. Antonio, A. Shomura, T. Shimizu, Okubo, K., H. Hori, R. Matuba, T. Niiyama, and K. S.Y. Lin, T. Inoue, A. Fukuda, T. Shimano, Y. Kuboki, T. Matsubara. 1991. A novel system for large-scale

286 @ GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

GENEXPRESS INDEX sequencing of cDNA by PCR amplification. DNA Sequence Chiannilkulchai, N. Bourg, L. Brenguier, C. Devaud, P. 2: 137-144. Pasturaud, C. Roudaut et al. 1995. Mutations in the proteolytic calpain 3 cause limb-girdle muscular Okubo, K., H. Hori, R. Matuba, T. Niiyama, A. dystrophy type 2A. Cell 81: 27-40. Fukushima, Y. Kojima, and K. Matsubara. 1992. Large scale cDNA sequencing analysis of quantitative and Rosier, M.-F., I. Reguigne-Arnould, P. Couillin, M.-D. qualitative aspects of gene expression. Nature Genet. Devignes, and C. Auffray. 1995. Regional assignment of 2: 173-179. 68 new human gene transcript on chromosome 11. Genome Res. 5: 60-70. Okubo, K., J. Yoshii, H. Yokouchi, M. Kameyama, and K. Matsubara. 1994. An expression profile of active genes in Rougeon, F., P. Kourilsky, and B. Mach. 1975. Insertion human colonic mucosa. DNA Res. 1: 37-45. of a rabbit [~-globin gene sequence into an E. coli plasmid. Nucleic Acids Res. 2: 2365-2378. Palazzolo, M.J., D.R. Hyde, K. VijayRaghavan, K. Mecklenburg, S. Benzer, and E. Meyerowitz. 1987. Use of Sasaki, T., J. Song, Y. Koga-Ban, E. Matsui, F. Fang, H. a new strategy to isolate and characterize 436 drosophila Higo, H. Nagasaki, M. Hori, M. Miya, E. cDNA clones corresponding to RNAs detected in adult Murayama-Kayano, T. Takiguchi, A. Takasuga, T. Niki, K. heads but not in early embryos. Neuron 3: 527-539. Ishimaru, H. Ikeda, Y. Yamamoto, Y. Mukai, I. Ohta, N. Miyadera, I. Havukkala, and Y. Minobe. 1994. Toward Park, Y.S., J.M. Kwak, O. Kwon, Y.S. Kim, D.S. Lee, M.J. cataloguing all rice genes: Large-scale sequencing of Cho, H.H. Lee, and H.G. Nam. 1993. Generation of randomly chosen rice cDNAs from a callus cDNA library. expressed sequence tags of random root cDNA clones of PlantJ. 6: 615-624. Brassica napus by single-run partial sequencing. Plant Physiol. 103: 359-370. Sikela, J. and C. Auffray. 1993. Finding new genes faster than ever. Nature Genet. 3: 189-191. Parrish, J.E. and D.L. Nelson. 1993. Methods for finding genes a major rate-limiting step in positional cloning. Smith, L.M., W. Hunkapiller, T.J. Hunkapiller, and L.E. Genet. Anal. Techniques Applic. 10: 29-41. Hood. 1985. The synthesis of oligonucleotides containing an aliphatic amino group at the 5' terminus: Pawlak, A., C. Toussaint, I. L6vy, F. Bulle, M. Poyard, R. Synthesis of fluorescent DNA primers for use in DNA Barouki, and G. Guella~n. 1995. Characterization of a sequence analysis. Nucleic Acids Res. 13: 2399-2412. large population of mRNAs from human testis. Genomics 26: 151-158. Smith, L.M., J.Z. Sanders, R.J. Kaiser, P. Hughes, C. Dodd, C.R. Connell, C. Heiner, S.B.H. Kent, and L.E. Hood. Pearson, W.R. 1990. Rapid and sensitive sequence 1986. Fluorescence detection in automated DNA comparison with FASTP and FASTA. Methods Enzymol. sequence analysis. Nature 321: 674-679. 183: 63-98. Soares, M.B., M.D.F. Bonaldo, P. Jelenc, L. Su, L. Lawton, Pearson, P., C. Francomano, P. Foster, C. Bocchini, P. Li, and A. Efstratiadis. 1994. Construction and and V. McKusick. 1994. The status of On line Mendelian characterization of a normalized cDNA library. Proc. Natl. Inheritance in Man (OMIM) medio 1994. Nucleic Acids Acad. Sci. 91: 9228-9232. Res. 22: 3470--3473. Southern, E.M. 1992. Genome mapping: cDNA Polymeropoulos, M.H., H. Xiao, J.M. Sikela, M. Adams, approaches. Curt. Opin. Genet. Dev. 2: 412-416. J.C. Venter, and C.R. Merril. 1992. Chromosomal assignment of 46 brain cDNAs. Genomics 12: 492-496. Sudo, K., K. Chinen, and Y. Nakamura. 1994. 2058 expressed sequence tags (ESTs) from a human fetal lung ~. 1993. Chromosomal distribution of 320 genes cDNA library. Genomics 24: 276-279. from a brain cDNA library. Nature Genet. 4: 381-386. Sutcliffe, J.G. 1988. mRNA in the mammalian central Putney, S.D., W.C. Herlihy, and P. Schimmel. 1983. A nervous system. Annu. Rev. Neurosci. 11: 157-198. new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing. Nature Takeda, J., H. Yano, S. Eng, Y. Zeng, and G.I. Bell. 1993. 302: 718-721. A molecular inventory of human pancreatic islets: Sequence analysis of 1000 cDNA clones. Hum. Mol. Richard, I., O. Broux, N. Chiannilkulchai, F. Fougerousse, Genet. 2: 1793-1798. V. Allamand, N. Bourg, L. Brenguier, C. Devaud, P. Pasturaud, C. Roudaut, F. Lorenzo, C. Tsai, J.-Y., M.L. Namin-Gonzales, and L.M. Silver. 1994. S6bastiani-Kabaktchis, R.A. Schultz, M.H. False association of human ESTs. Nature Genet. Polymeropoulos, G. Gyapay, C. Auffray, and J.S. 8: 321-322. Beckmann. 1994. Regional localization of human chromosome 15 loci. Genomics 23: 1001-1009. Uchimiya, H., S. Kidou, T. Shimazaki, S. Takamatsu, H. Hashimoto, R. Nishi, S. Aotsuka, Y. Matsubayashi, N. Richard, I., O. Broux, V. Allamand, F. Fougerousse, N. Kidou, M. Umeda, and A. Kato. 1992. Random

GENOME RESEARCH@ 287 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

HOULGATTE E1 AL. sequencing of cDNA libraries reveals a variety of (Gene Product). In new (E) or overlapping (F) expressed genes in cultured cells of rice (Oryza sativa L.). subsections, "DNA region" or "overlapped gene" Plant J. 2: 1005-1009. refer to the gene product name having an iden- Walter, M.A., D.J. Spillett, P. Thomas, J. Weissenbach, tical or overlapping sequence, whereas "similar- and P. Goodfellow. 1994. A method for constructing ity" and "gene product" refer to the true func- radiation hybrid maps of whole genomes. Nature Genet. tional similarity of the transcript. 7: 22-28. "Tissues" indicates the origin of the cDNA partial sequences, abbreviated as follows: (AE) Waterston, R., C. Martin, M. Craxton, C. Huynh, A. aortic endothelium; (BC) adult brain cortex; (BO) Coulson, L. Hillier, R. Durbin, P. Green, R. Shownkenne, N. Halloran, M. Metzstein, T. Hawkins, R. Wilson, M. adult bone; (BR) brain; (BS) brain striatum; (CC) Berks, Z. Du, K. Thomas, J. Thierry-Mieg, and J. Sulston. colorectal cancer; (CM) colon mucosa; (EK) epi- 1992. A survey of expressed genes in Caenorhabditis dermis keratinocyte; (FA) fetal adrenals; (FB) fetal elegans. Nature Genet. 1: 114-123. brain; (FI) fibroblast; (FK) fetal kidney; (FLS) fetal liver and spleen; (HA) heart atrium; (HE) heart; Weissenbach, J., G. Gyapay, C. Dib, A. Vignal, J. Morissette, P. Millasseau, G. Vaysseix, and M. Lathrop. (HG) HepG2 liver cell line; (HI) hippocampus; 1992. A second-generation linkage map of the human (HL) HL60 cell line; (LF) lung fibroblast; (LI) liver; genome. Nature 359: 794-801. (PI) pancreatic islets; (PL) placenta; (RE) retinal pigment epithelium; (RH) adult rhabdomyosar- Wilcox, A.S., A.S. Khan, J.A. Hopkins, and J.M. Sikela. coma cell line; (TC) temporal cortex; (TE) adult 1991. Use of 3' untranslated sequences of human cDNAs testis; (TH) THP-1 cell line; (UN) unclassified. A for rapid chromosome assignment and conversion to STSs: Implications for an expression map of the genome. few gene transcripts were found identical to short Nucleic Acids Res. 19: 1837-1843. genornic sequences such as STSs and were classi- fied in the "known gene transcripts" subsection, to show their similarity, even though they Received July 13, 1995; accepted in revised form September should be considered as new gene transcripts. 28, 1995.

APPENDIX 11: DATA BASE CROSS-INDEXES APPENDICES: THE GENEXPRESSINDEX Indicated are accession numbers (A) or eSTS Only a small fraction of Appendices iD and 2A-B markers (B) linked to the different gene tran- are shown in print as examples. The remaining scripts. The first column (in bold) indicates the parts are available as an electronic supplement Genexpress Index number (GENX). Accession together with the full text of the other appendices numbers correspond either to Genexpress se- at http://www.cshl.org/in the Genome Research quences (normal typing) or sequences from other section. Please follow the links from the home groups (accession numbers preceded by #) page. present in GenBank. The different columns for eSTS markers indicate the Genexpress Index APPENDIX !: FUNCTIONAL SIMILARITIES number (col. 1), GDB D-number (col. 2), se- quences of forward (col. 3) or reverse (col. 4) Classification of each gene transcript has been primers, and expected (col. 5) and observed (col. designated as Known (A), Homolog (B), Related 6) sizes for the genomic PCR product. (C), or Unknown (D) on the basis of data base similarities. A special classification was necessary for Overlapping transcripts (E), or New tran- scripts in known (already sequenced) regions (F). Information available in Appendix I are the Genexpress Index number (GENX), the clone fre- quency in muscle (% muscle) or brain (% brain) libraries, the number of partial cDNA sequences registered in public data bases linked to this gene transcript (Seq), the chromosomal localization obtained with Genexpress eSTS markers (eSTS), or already available in GDB or GenBank (Map), the species (Species), and gene product name

288 dl GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

Appendix 1A: Known gene transcripts

GENX % Mum=le % Brain •nss ,~. eSTS' I~,,,R . ~ product = 2.~, ,, 3 HE 14 ' 14q11.2-q13 cardiac muscle bete.-m),o~n heav~ chain 3 0.09 0.06 2 HI~I~, 3p~ Rh~ 6 0.01 ,, 8 =ut~nic a,hyc~aca.~eiated ixo~ 10 0.01 1 Pr.e-B call e~hansing 1actor .... 1| 0.01 3 I Prolilin 2 , 33 I 0.01 1 ~I.~,~ ~u~,~oan~,.te ~p-~ss ~.i " ,' ', 42 0.01 $ TH, BR~I~ h',~tme H3.3 SO 0.05 i r,qlr,-~ neutoendm~rino ¢onvertsse I .... ~1 0.02 4 i HG;FI~,BR" 17p13.3. PAF ~ h~olue . , - 0.oi mitochmdtkd marx p,'otein PI . o.oi 15<126 ...... o.os I 2 iniliailm factor 4A-I , , 163 0.01 ! lq2S~131 hi.in B2 114 0.0~ 1 FLS • 0 .p.o~.,.~o~e ph~o~,te;,, d.,,, 121 0.07 6 HL~HI,FB,BR 17 1~q~s mptalopro~nssa inhibitor . 1~ 0.02 2 HI~BR 19¢]13.4 ,protein kin m C ~amma 125 0.02 3 I HL,BR, FLS ¢~ml~ aampled cDNA D31767 s,~ ...... O.Ol 2 HLfI~R , relSte¢l I~yl-tRNA synlhetese m ~.oi 3q13 UMP synlhlae 176, ,, 0.01 NOT, 191 0.01 1 1p21 ocllogm alpha 1 (Xl) 192 0.02 gravin ~.. 0.Ol 2 HL~BR 21~2.3 ~9~ alpha,, I (xv,,) 198 0.04 0.01 5 CM,HI~BR 12, 12p13.3.p12~3 a~a 2 macroglobulin 2O5 0.01 1 , , ,,, 53PB2 p53-bindn~ protein,,, 2:16 0.06 I HI c-inexin 238 0.01 Xq28 bone/~rtlage' proteoglycan t precursor ..... 262 0.01 TGF-bete reeeptor type 3 277 0.Ol , 13q13 ceuine kina,r,~,.,., 1 , 2~ ...... o.oi 6p24.2-p23 endo~elin-1 271;I 0.01 lS~4-~zs ca~p=. H ~m ,, o.13, o.oe' is I~IL,FB,HI~PI~BR X+3+4+7 elon,~ation betor I ~jamma 314 0.03' math ~fmelonate-semialdeh,,yde dehydro~enase 317 0.04 0.0t I BR 3p21,1-p12 , I non-speci~c delta.amino ievuiinate synthase 1 334 0.01 17 ,STS UT228 ...... 341 0.02 2 CMrBR B12 protein 344 0.01 ,I, HI. 8q24.12-q24.13 ; c-myc p'oto-anocgane ,, , 350 0.01 r G25k GTP-bindin(j proteinl,brain isgform 387 ' , 0.0t , g HI~BR 8p21 dusterin ..... 361 0.01 11 ql 3 phospholipase C-Beta-3 363 0.oi ...... ; ~ ribosomal protein L7 374 ,0.01 1 FIG 16p13.t =GST1 -HS GTP-t~n,~din,q protein 380 0.01 1 BR ,17 17 re#ica ",l~n Pro,t,~ n A 70kD DNA-bindincj subunit 387 0.02 , ~ .... 16od?.2.1 ¢elretinm 391 0.03 I~/'.~; i'] | Ill, i]] IT:]~:I I I1 { I[*il |:] 1]~:~ [:] I[:~:! 463 o.oi .... ! ~,~, 3 ocammer ~m~ex 4oe o.o2 1 CM 6p?.1 2-p21.1 meth~malonyl-CoA mutate 410 0.08 1 BR 11,, , metabotropic, ~lutamate receptor 5a 424 0.02 3 BR ...... ofiP binding protein ( ,OBP-2~ .... 441 ,, 0.02 2 HI,FI , 6p21.3 antigen pep~de transporter 1 443 0101 1 ,, ...... DNA M82819...... 452 0.02 4 HI~BR high mobility 9roup prote~ HMG1 454 0.01, ,, 4, HGrBR pr~ ph~phatsse-t .qamma 1 450 0.01 1 FB 17 :)soriasis-associated fatty ac~l binding protein homolocj 4~ 0.02, 4 HI~BR 8p21 neurolilament sulounit NF-L 474 . 0.02, . 1 HG mitochondriel 63S ribosomal p,.otein 1.3.," 483 0.04 0.01 1 STS UT5790 492, 0.0i 1 5 5q31 dinudeotide repeat polymorphism at locus D5S178 507 0.01 21q22 91utamato receptor (GLUR5) 813 o.o2 , 6914-q21 5:nudeo~dase precursor s21 0.Ol beta-arres6n 1 54,9' " 0.0,1 , 1 HI 7q22 cAMP-depend,,ent protein k~nase 2 beta re

289 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Appendix 1A: Known gene transcripts (continued)

874 0.04 0.03 1 BR calmoduli,n-~ndent calcineurin A 877 0.01 randomly ~m~ed eDNA D28475 .... 901 0.01 ¢arbo~yl methy~rans.(~ase ..... • 0~ 0.02 I HL ,, 21q22,,3 e-ETS-2 ...... 914 0.02 2 BR 11q.~3~, 3 T~-I 915 0.02 2 CM,FA ik~..3.1-~ fa,ne~yi-dinhos~ate farnes~4nnef~-=e ' Sm o.02 21q22.1 interferon gamma reeeptor,bm, a chain ...... 900 0,02 1 HL 140123' Max • /2 0.09 0.05 10 HI~BR I 117/' 0.01 , prota~ phoephatase PP2A 55kd' regulsto~ subunit neuronal isofon~ ...... 98O 0.01 2101 STSin D21S337 DNA marker m ...... O.Ol s ~.!,L! 950 0.01 B~4 protein ,1017 ...... 0.01 , ,, 10~2 0.01 u i p36.1-p35 sodium -lOtoton exc"han~r, :I "' 1033 0.01 .. ~r.r~-qwr, e~in ..... 1045 0.04 0.01 4 HL~FB~FI.S~BC DNA-bindir~ protein 1062 0+05 1 BR .... 4gH-q12 PDGF a~h~re~, ptor , 1080 0.0,1 2 I BR 17 granulin ..... 10B8 0.01 11)31 medium..chein acyl-CoA dehydrogenmm .1104 0.13 8 Fe,,BR ,, , 61)21.3 ~u~n be~1 .... 1108 0.02 3 FBoBR MADS/MEF2-famIIy I~mscdpllon f~c'tm MEF2C i115 0.01 6 $.8dance~methionino decarb~sse I 1118 0.0t 5q34-q35 GABA-A reoK)tor eiphl I i~10unit ...... '1119 ' 0,01 1 HG 1 I¢112 hig.h.rnobil~ ~roup ~ ,SSRPI ...... 1121 o.,Ie o.o5 2 'H~ 1 lq21-~,, ,, m)dium-pom~um ATPalm elldm2 , 1129 0,02 4 HG~HL~FB ..... ma'orl nudear, malnx Protein matdn-3 ,1141 0.03 5 HIIPI~BR , , 14-3-3 protein ,theta ,,, 1,142 0.0i ...... 100111.2 ret p'oto-on¢o~ne .... 1146 0,01 seoreto~anin 2 ,,, ,,,1~,S1' o.oi , , , 191)I 3.3 guanine nude~de-bindin 9 Protein C-,(y)alpha ...... ,~,~50 O~Ol 1 OR Ir~,ot-mpeat containing cDNA CTG;,B37 1161 0,01 ...... 190113.2,¢113.3 DNA li~ase I 1175 0.01 Xq25-q26,1 Lowe's eculocerebrorml syndrome protein 111)6 0.01 3 FB 2 pro~hp~o~n a~ha . 122S 0.01 Sq22-q23 ~,~ndecan-2 1234 0.02 , 5 HG~FBtBR motor proton 1~o 0.0i .. , . I~p13.2. R~b-3A 1249 0.01 ~m~p~o. fqotor HTF4A ,,,1,~o 003 .... 3 BR,P! TPA-indueibie c54 mRNA , 1250 0.01 ...... ~ h,~.,,, ~CK 1 380 0.01 kmppel zinc ~gor LDR152 1385 0.02 IOq24~5 Mxll 1238 0.01 1 HI. ... M~.k4Agone(d.~oT33) ,, ' ' 1319 0.01 aeparty0 be~-~ox~m, 1325 0.02 1 BR Bd-xL 13410.13 0.01 13 i HI.IHIIFBrP' ,,20 ~13.2.~13.3 9u...,in:.ud.o~*-~,~ ~.).~ph: -,,-,.~ 1342 0.04 0.01 1 I BR 1 lql 3 protein phcephatase PP-1 ,,Ipha , 1.o o.oi i p~ RSU-1 ..!~ 1 ...... 0.01 , , 7 sorcin SRI 1380 0.04 0.01 9 HI~BR~PI ADP-ribosyl~on factor 1 1382 0.01 19p13.3 lamin B1 1407 0.02 1 BR 161)12 protein kinane C beta 1411 0,01 1 FB ¢edherin 13 ,~,m ..... o.ol ..... 3p26-p25 plama membrane celeium ATPa~e brain kmform 2 ..... 1434 0.01 ,, cAMP-ceeponee el~m*nt bineing Pro~dn CREB 1450 0.03 4 OR dome 1NIB210 from infant brain 1458 0.0~ I HI 16(:113 .... ~,l.mnlnenude~i, "de-brndin.g proton G(O) alpha 1484 0.0~ 2 BR ,, , ,, I L:~en-cj21..... ~apIotagmin,,1 ' 1472 0,02 CD83 1461 0.03 15<111,,¢113 g=~,,,m,,a-aminobutydc-add r ,e~ptor ~ha-5 ~bunit 1462 0.02 1 BR 5933 ~lul#melm receptor subunit GluH1 1,m 0.02 21q22.1 phos~oribosylamine-glycine ligase 1,40~ 0.0,, 0.02 2 H~;e~ !,7ql 1.2-qi, 2 thyroid hormm e receptor alpha 1488 0.01 61)21 , HMG-I(Y) 1501 0.01 Xq28 gluCo~l S-phosphate 1-dehydrocjeneN ,,,,1,Sl,o ...... 0,01 ,1 BR 14q22-q24 lISP70 protain 2 1522 0.01 17q25.1 paoxisomei fatty acyl-<:oA o~idase '1528 0,01 20q12-q13.1 DNA topoi~m~raN I 1529 0.01 2 HLrHI ,, 20ql 2-q13~1 ribophodn II 1S30 ,, 0.01 1 BR rando~y saml~'~;dcDNA D14695 1542 0.02 1 SR Igp13.3-p13.2 comldement C3 1S48 0.01 STS UT5029 1549 0.02 3 BR CLA-I 1003 ,, 0.03 ,2 ;FBtBR 22q11.2 cjuanine nude~de-binding protein G(Z~ alpha 1572 ,, ,, 0.01 acliv~n receptor type II ,,~,s~4 ..... 0.02 sterol r~latory elemant t~nding protmn 2 1381 0.01 growlh-m'rut-epeciJ¢ proton i~ o.o~ o.oi ' 11 !1q24.1 doddng protein alpha 1~89 0.01 2 P I;BR 1~1,12.1 ! lronslhp'etin ,1,SN , , , 0.01 2 HL~BR 11 q~3.~5 emylo~d-like protein 2 1602 0:01 1 BR randomly Hmpled cD,NA I:)21064 1606 0.09 0.02 4 FB~B,R 2+10 , ,, ,, ac~n-related prolein 1010 0.01 1 BR ~113-~,* aJpha-N-a~/Iga faoto~minidue 1630 0.01 1 FB sp12-p11 DNA pdymeraH be*: ',,!~m ...... o.os , x X membrane transport Protein XK 1M3 0.01 'I B R' rho GDP-diem)dal~on inhildtor 1 1644 0.02 T-coml~ex protein 1 gamma 1(~0 0.02 h~tcne H3.1 1~ .... 0.02. mannos, 6-phos~ate k~merm 1663 0.01 autom tigen PM-SCL ,1~2 0.02 I HG i'~:p31.~',' gl.ce.e ~an~oor~- 1 or~recytarorein 1603 0.01 I AE,, , , caldesmon 1705 r 0.02 ,1 B R ~ght junction protein ZO-I 1713 0.01 13q34 liver proDin similiar to #9 ,hepa6c,protein 1710 0.02 3 BR phoephodiesmrase gone .~72o ...... 0.oi 12q13 early response protein NAKI 1723, ...... 0.01 2, ' BR 17 pp'r oline-5-carbo~late reductaso 1,727 ,, , 0.01 1 ~I,.fl.. done 76 mRNA ...... 1,753 0.01 2 FB 14~2.3 aoetine kina,=e B ...... 1 ~ 0.01 1 HI. randomly ,s~mpled cDNA [:)25538 1780 0.0t 2 FB 21 sodium channel protein brain I alpha subunlt 1783 0.04 ,0.01 6 cetion-indepandent manncee-6-phcephat, reoeptor 1785 0.01 :~o22-p21.33 beta ¢jalectceidace 17~ 0.01 91)21-p12 a~iei nalriurelic peptide receptor B 11~)1 o.01 2 FBrBR be~5 11123 .... 0.01 1 BR finger protein HF.12 1828 0,01 1 BR '11p13 paired box protein PAX-6 1835 0,02 aq4 =ulfotrans~ase 1850 .... 0.01 2 erythro¢yte beta a dducin 1as2 0.02 '1...... FB hnRNP complex K 1866 ,, 0.01 2 BR ! trmsmembrane receptor Rorl 290 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Appendix 1A: Known gene transcripts (continued) ;~p25 red ceil acid phospheta.se I 1872 0.01 trma¢ipSon lector LSF ,, ,,, 1681 0.01 5¢123.3-¢131.2 llyS~lOX~I 1006 0.02 4 HG,RE,BR 3 3p25 ~d~omoseme 3p25) membm~, Promln 1¢00 I O,O5 olycine dehydrocjenase +~0 II 0.01 2 Hi,BR I I I 22¢]11 TUPl-like enhancer of If~t gene 1 ~ q.Ol 14¢[24 O-I :,telrah~a#~,,te lynlhsee olttoplasmic 19S1 0.09 0.01 1 HI 2 ONAJ proton homoiog HSJI 1~ , 040t .... " 4 glut,amine PRPP amidol~ansllmase IM5 i 0"~ 1 e~ ll ,, mg GOS lm O.Ol ll 1NO 0.02 2 FB,BR 1070 0.01 I lq31 laminin 9ammlP1 1~0 0.01 3 FS~BR ~I 3 I miaotubule alMo~llled,pTot~rl I O 111~ o.og 0.01 1 BR iniliaSon |aot~' 4 ~mms 2001 0.O1 2OO2 0.01 2003 0.01 int~rin b~ta 5 3004 0.01 B70 andgen 0.01 2 HI J ,17,~1 g~., ~ ,~..y ~ Pr~n,,, mm~ o.oi 4 ST~1-666 2010 0.01 1p13.~ mu~dieg~m~.~ S+~;~;mse 0.04 0.02 3 3022"1=23 miemal~-h repak protein hemok~ ~l ~! 0" ~0 2045 0.01 , steroid hormone mc~ptot ERRI .... 2051 0.01 I ~PI 17¢125 protein disulfide ie,amer~e so~o o.o~ 3 i~, "R ' rlndomly ~m~ed eDNA D21250 ~o~s O.Ol 22 14-3-3 protein eta I HG HSP70 0.04 0.01 i HL HLA-B-seseciated tranr~i~ 3 2ge6 O.Ol 1 CM 11 p15 tumor auppreseor HTS1 ~02 o.oi 2110 0.01 I BR Xp21.1 RP3 ]l 2118 0,+02 2 FB,B ~. I I I .... ~8 ~1 au~n~ V ~ p~l illlllll II i I i =I~ i 0'0~ + l BR ii i~m~ TMd~in li~t ~ ~ ...... 2125 0.13 0.01 6 HG FBBRrR H .... a dic ribosomal phosphoprotein PO 2133 0.04, 0.01 2 BR 7p13,p11.2 2-oxocjlutatate (:ksh~dro~enase E1 2135 O.Ol,, activator 1 37kd subunit 2137 0.01..... 19pll3,3 u~qt~tin ~ga~n~ enzynle 2~4~ 10. ~ 0.01 l+ CM 1 call,a in 2 kuge subunit 2146 I 0.011 ,l I ..... BR 7q35 aldose feductase I 2147 0,09 0.02 II I PI 1+4 lq22.q25 , sodium-pc, teseiu m ATPase beta-1 2154 0.01 protein ~hsulhde kmrner~e.rei, ,ted protein ERP72 21~ i 0101 ...... I 5q22-q32 monocyte diffel.~ic/asonanhgen CD14 myoblast cell surface antigen 24.1D5 I' BR I ' .... I I ' I 2204 0.01 1 I 1 ~I 3. t ..... receptor ~p~ne k~a~ UF 0 l* 22O6 0.02 IL2 receptor eipha-chmn kappa G ~nding protein ...... 2211 0.02 21 HG.BR 7~ I ! hepalic leukemia tactor 2222 0.02 8q21 3-¢122.1 , call0ir~lin 1 2223 0.05 .5ql 3.3,qi 4 3,hydroxy-3-methylglu.tm'yI-CoA reductase 2227 0.01 FKBP-rapamyd n aaseciate.d protein FRAp ...... 2230 0.0t ,, 1 HI 4q26-o,28 .. a.nnexin 5 [...... 2232 0.02 .6p2,1.3 .... HLA.B-associated transc6pt 2 12242 0"0~ .... 3q21 ~ ribopIlorin 1

224~ o.oi 1 HA .... Ill .i randomly sampled cDNA D14664 2258 0.01 2 BR DAP-kinase 2259 0.04 0.03 s PItBR~FA tidal I ' eipha-amida5 monoox enase ...... 2270 0.09 0,03 , 1 BR rat fm~:! ,q~ne RFG (RETI/~,TC3 ~ II [ 22B0 0.02 I t BR ...... gr~ |a¢to~,r,~,o~,,~or-l~:)uR,d protein 2 l 2289 0.01 . L-sedne dehydratase ...... 2~ 0"05 c~clherin 8 2295 0.01 I HL I~oi ~:'~p13,2 DNA Ic~tosine-5 ,)-pethyl-~'amderase ...... 2296 0•02 4 ,, BRrTE i leucine-rich 130kD protein 2300 0.09 0.03, I 3 FB,BR i 16 16p12 mitoahonddal ubicpi .npI-cytoch~ome C reduc.taN cOre protein 2 2319 0.01 ...... t q211.i1 high affinity immunogloloulin flamma FC receptor 1 2327 0.01 9 .... 9~ .... pIasma ...... ~e~n ~ ...... I I 233O 0.01 , pr~ein phosphatase PP-2A 130k,J:ire~ulatoQ, submit CM~PI 13 smart ribOnucleoprotein U6 2365 0:01 ,, 4q24, TGF I ~,,re-3 ' 2360 0.01 ...... , , 16p DNA-3,methylado~ne glycosidose 4qi 1-q21 I ostaopontin 2376 0.01 x~o,25 STS sWXOSgS 23B2 0.04 0.01 3 ...... ;, ~...... nud~c ~d U~"~ Ipr o.in (CNBP~.. 2381 0.01 1 BR 14 2399 0.01 I BR par.neoplastic ¢erebeiiar do~,enewetion-associated antigen 2412 0.0t 9 CM,BR ...... ~21 l l l pol~.SJ~'us protein I . 2416 0.01 I ...... 7p hexokirmse D 2439 0,01 1 FB '1 .... 16q13,~I DNA-dimcted RNA pdymerase II 33kd pdypeptido 2440 0.04 0.01 13 I~4 ,,icollagen IV alpha I 244S 0.02 2 inte

2506 0.05 I I I 6 CM~FBIHIIBR ...... AlzheimeCs disease arnytoid A4 protein 2527 0.3i 0.02 I BR 12 i i I ~ ~'q32[ ~ I 2536 0.02 1 BR arr~inine-rich nudeaf prote~ i I 12MO I, 0.01 lq22 q24 Ski arlene 2543 0.04 0.02 21 papillome~ms E6I Ol~eni¢ protein a~ociated Pro~n 2554 0.06 6 BR ~7 i ~Tp 113m3 guanine nudeotido mFplatory protein ABR 2586 0.01 II 7~ I J ~ ~x~n~ ~ 2 i ~1 2588 0.01 ...... male enhanced emtige,n,(Me,, a 1 I 112~ 0101 1 FSl gl~can 2602 0.01 1 BR I 7ql 1.2 NADPH-cytochrome P450 reduotase l l2~ 0.02 1 reldication Protein A 32kd ~ubunit (RP-A) I 2611 0,01 I I I ,~ .... I bask: ~ranscnp~on factor P62 2616 0.13 0.05 1 BR 4 CDC2-related protein kill,la .~ (P!SSLRt=) ' 2~1e 0.02 3 HI,BR ' i'~13.3' bas~in . 2625 0.0t 3 CMIPItBR , Ip34, tAR protein ....2~2 I 0~01 II tl BR T ~l~l i ii~ ~?in~ *l~ iO~ n • ph ~ha ta~ I 2547 0.02 2 BS~BR II 115 STS D~78 ~i~ CA ~F i i 2~1 0.0~ ...... ' putafi,/e receptor ~otein I I II , ,,, , ,,, , .... X+7÷12÷.~.,4...... initiation I,act~x4B I r I 2674 0.01 17p12-p11.2 periph~al m~Dlin protein 22 ...... 2676 0.01 ...... 7q36 homeobo~ protein EN-2 2~ 0.01 1 ~l ...... ~e m..orphogenetic Protein 12B ll ~ 0"0~ H3aS mRNA .2¢02 0.04 0.02 3 ,HL:PI,HA 17 17q23,q24 I~M, p~rl|lpToleinl~inase 1 alpha recjulalory ~ ...... 0 .~ U2 sm,eil ribonudeoproteln B" , 0.01 1 BR 6p21.3 Gge ...... 291 Appendix 1A:Downloaded Known gene from transcriptsgenome.cshlp.org (continued) on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

270~ 0.01 4 BR,PI 10 43 kd inos,tol polyphosphate 5-phcephatase 2~8 0.04 2+10 20cen..ql 3.1 S edenosyl-hornocysteine hyd¢o~ase 2726 ,0.02 2"' HG',BR p~asma 91uta~one p~o~idase 2728 ,,0.13 ,,, 6 6q22.1 card,~c phosphotamban 2730 ,0.04 13op4 co~gec w alpha 2 2731 0.09 1p13 AMP de~mase 1 .. 2732 1.01 1 Pl 119 ..... 19 ca!pain small subu~1 ..... o.04 -. 4 T-cell specific tyrosine kinase 2741 0.()2 12qi I -¢]I 2 contac~nI 2747 0.05 10 randomly r,m~npledcDNA 031883 ..... 273S 0.01 ,~ ,,~ ...... tyror~ne kinase recepto~ HEK2 276~ 0.02 X~24 Iysosornal-tassociatedmembrane ~),cop'otein 2 2781 0.01 Xq21.1-¢121.3 Znf6 2~ 0.02 4 HLrBR,CC 1p31-.p32 epdermd growth facto" recepIo~: r,~Jbstram 293g 0.01 I HA skele~ muscle 165kd protmn 2861 0.03 I BR 026350 ino=;tol 1,4r.~Vipho~p~ate type 2 receptor UNK. 2862 0.01 r~prem-mnsiWe 3"*5' phcephod~e~e~aea ,, 2.872 0.01 19pI 3.2-pi3.3 N-ece~4gkJCOSam~e receptor 0,04 0.03 2 FB,BR ~tochrome C ,, , ~B~I 0.01 17q24-q25 edre~o~ine¢~Ioreductsse (NADPH 1 2¢O2 0.01 4 4 STS 4-1312 2915 0.01 1 HI 17¢[21 prohibi~n 21133 0.01 7q21 mulbdrug re,~stanca protein 1 21~7 0.01 sdrenom~du,.i,n 2945 0.01 1 HL b'anslormUon-sanb6ve protein IE.F.ssp 3521 ...... 2950 004 0.02 3 BR, 4 4p16.3 e~ythrocyteadducin alpha subuniZ 2956 0.05 I BR 17 done KDB1.2 with (CAC~n/(GTGp repaal 2957 0.01 4q25.q34.3 glutamate r~K:eptor 2 29M 0.O6 4p16.3 neurorPspe¢ific protein ,29~5 5.10 1 FB lq42.1-q42.3 adult sketetal suede alpha-scan 21167 0.02 18 18pi 1.2 receptor.like prot~n-t~rosine phosphaler,~ MU 2972 0.22 feel skeieta~ muscle troponin C 2973 0.05 im BR 6 melate oxidoredu¢tase 2979 q,o,1 lib ~uppal-~,pa zinc fin(jer 2884 0.13 0.02 Im CC lg n.atural killer cell enhancin,q factor B 2~83 0.09 0.03 Im II HG~HIrBR 4+6+8 6p21 HSP.90 be= 3000 0.02 hMCM2 3006 O.13 0.07 7 RE,BRrPI,FI voltege-depe~dont anion channel isoform,, 2 3013 0,16 2 FB,BR 5 5¢121-(~2 edenornalou ! pd~o,,=s coli protein ..... 3015 0.06 3 BR,Pl 4 synudein 3018 0.04 0.08 1 Pl 4+7 4 randomly =rumpledeDNA D25274 3o~s 0.02 ndfl 9 neu differenciation factor 3028 0.04 0.O8 4 HLICM,HliPI ' ' 6 6p21.3 HLA.B 30~0 0.02 3 PI~BR ADP-ribos~4abon fe~ 4 3051 0.18 0.02 4 4¢135 skeletal musde ADP=ATP carrier protein 3060 0.04 0.09 12 HGIHL,FBrHI~PIIBR,Ft '+3+4+6+14+; ribosomal protein L10 ... 3061 0.03 2 HI,RH Xq28 CDM .... 3067 0.09 0.05 3 HLr HI 2+17 ubiqui~ (3 repeats) 3071 0.05 randomly sampled eDNA D29643 ,,, 3078 0.02 randomly sampled cDNA D29958 30~e 0.02 BR loq24.q25 elphs-2A adrener,q~creceptor 3108 0.09 0.02 FBrBC,BO 9+11 11pt5.4 hemoglobin beta 3125 0.02 Xq21.3-q22 BTK re(jion done ftp-3 3145 0.04 0.03 HL, FB 2 2ql 2-qter nucleolin 3147 0.05 7 beta-2 ¢him aerin 31M 0.03 19 .... 3160 0.02 12qi 3 transmembrane 4 superlemily Protein SAS 3181 0,02 BR randomly saml~ed cDNA D21262 3164 0.03 Ht,BR 17 fructose biphosphale aldolase C 3167 0.02 FB S-a0mnceyIme~ionine sptheteae ~amma isolorm 3~7o o.os BR 6p21.2-p21 .I factoykjlu~atone lyase 3174 0.02 2cen-q13 Rat.related protein RAL.B 3176 0.02 14<]32.33 Ig Mu chain C 3183 0.03 HLrBR 1 6p21.3 HLA-E 3i87 0,02 HL 12p13.3 gJucose,transporter type 3 31110 0;03 ~BR 17ql 1.2 neuro|bromin 3184 0.04 0.01 BR 9+17 NRF1 protein, 3185 3.38 FB 19 19<]13.3 =oibne kinase M 3198 0.02 ... extracellular Wclnal regulated kinase 3 (ERK3) 3207 0.03 I.ocal adhe~o, kinase ... 3212 0.03 BR 91utwn.ate tr~sporter"'D26443 ' 321s o.02 5p11-p12 zinc finger ZNFf 31 3219 0.35 2 2q33-q34 skeletal musde myosm l~ght chain I and 3 3230 0.05 FB,Pl 4p14 ubic~Im carbox~4-terminalhydrolase isozy~ne LI 3237 i.19 1 Iq13.1 muscle ¢jlycoqen i>hosphor~4ase 3~s. o.o8 8R 12 I ~.ioulinalpha 4 3248 0.03 HG~BR 3p21.2-p21:;! inter-alpha-'a'ypsin inhibitor complex compp.nant !1 32S2 0.01 1~112 , RNA pdymerase II 14.5kda subunit 3250 0,O2 12q13 .ce.l! dive,on pcoteinkinase 4 3272 0.04 19 suede c~ochrome C oxidaca 7A 3274 0.04 0.03 HGrPI.BR HSP-90 alpha ,,, 3275 0.02 BR ,, 2 2q33-q34, IGF bindin 9 protein 5. 3284 0.03 HI~BR 4 4 carboxypepbdase H 3306 0.03 18pll.l-q11.2 aIphs-2-p~awnin inhibitor 3316 0.02 I q41 -q43, 10..myo-ino~lol-briphOsF~ale 3-kinase B 3321 0.02 BR,FB,HI 6 T-complex-auociated testes expressed 1 homolo

292 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Appendix 1A: Known gene transcripts (continued)

3427 0.40 3 ,~ BRtPI=FB 16 DNA-be'~dm9 protein A 3430 0.92 0.05 19 I BR,HI,FB,PI ,12p13 91ycataldehyde 3-phos~ate dehydmcjena=e 3436 0.04 , 8+13 histone H2A.Z 3438 0.22 1 HI_ 8+18 non-urcomeric myosin "tl

4O73 0.02 i>u~ve ~Hxine/threonine-protein. kmase p78 , 4O77 0.09 HG yea,,r~,ribosom,dprotein $28 .homd.opue .... 40B1 0.02 randoml~ lemp4ed cDNA D30756 ...... 40B6 0.03 2 BR lq~.I MAP kinase phol~ohatese I 4~8~ 0.09 O.01 4 HLtEK=HI x xq13.3 , p~oho@/,,'erate k~na~ 1 4104 0.04 O.01 2 HIrBR 14 nu~aosoma aasemb~y protein, , ....~105 0.09 .... 3 ' ~,F","R Ip~.t~5 m~h~in ...... 4105 0.05 1 BR 4 a~tor ,,1 140kd ~bunit 4119 0"04 0.05 2 BR 10 1(~24.1-q25:1 aytoac~c aq:~rtete aminotrem~am 4134 o.05 HG~HI~PL pep~pro~ne cis.~ans isomerale A ...... 4137 0.~, 1 MAC30 4138 0.09 0.03 iso4euayl-InNA syn~etase 414,9 0.04 0.01 3 CM,PI.CC done lee10 m RNA 4156 0.10 3 HI~FB~BR naum~

5276 0.01 1, r,,andom,Iy sampled cDNA D31891 ,, , , ,, ,~04 o.oi 15¢111.2.qi2 g am ma.aminobuty..ric-acid mcept~' beta-3 zubunil, ~319 0.01 helix-loop-helix basic phoephop~otein ,,, $322 , , 0.01 ,10q24. nuclear.b,¢1o~ NF-KAPPA-B Pill) ~M ...... o.oj ',a ~,Sn '.: in..tagrMmlm~br~ne ~otain Eta !,m .... o.01 4p 'r;~i~ly ~pledl, c~NA 025250 ' o.01 i HG',FS 22 X-bo~ lin¢in 9 i~otein • T#0 0.01 l~

5570 0.01 I ap22 iipep'o1~n Ip~m ~5580 0.01 5 CMIBR, FLS 1~c~4.i-q~ ~F~e~m~ 5597 ,, 0.01 :2 CM~BR , ,, ,, Ip~2.1-q~r ~u.~nata dehtd,~n~se I,~none) lavoFote~ mbunit . s~01 1 , o.oi 11p15.4 ~hk~mv~ina ph~aea 5602 0.01 • ana~min 9 ~ ~a¢~ induced prota~ .10 0o1 mml~ , Xp22.3 ..... GSI protein of unknown funcion S623 0.01 1 ;BR 10 CpG done AS ,,, , ,. , ,S~,~ o.oi 2 I FB~BR ...... 14q protein fatnes~anafereae bel tubunit , ~I 0,01 3 ; HLITE Protein.~oine phcepMtase GI ~8 ..... 0.01 1 CM 20pter-p12 proi!Mral~ cell nu¢lea~rqnt~en ...... S~?o 0:01 m~ tr,anaformationTr elated protein ,, 5674 0.01 Ir~s.~, h~n , , ~== O.Ol mid• 3q13.1-q13.2 rmuromodutin ,..,~187 0.01 13q32 ,DNA ,r,eL~,ir Proton complemanl~n~ XP-G cella ..... S694 0.01 1 HL , ~ si~iciqg

HOULGATTE ET AL.

Appendix 1A: Known gene transcripts (continued)

[,x,~mm IIIII III mi~rosornal x',:le h drol~.e m [~,~- III I mm,mU~:i i illlllli IIIIIII hnRNP h? m°l. m L,x,:m IIII II ni ribosomal ote~n ~~30 horn m _ aden atebindl o~n m [,X,~! ii|j ~. T-c~n m oteinlal ~s~0cmit m [;~;~'i i/i'~:' IIIII III m ~,,x,*~m II 6 [,x,;~mmmx,~m I IIIIIIII HLA-A m [,x,zm III IIIIIIII 17pt~-pll1 ~-p 11 ~eletal m~e ~ ~ hew ), ~/~in m [,x,zm D' I:~Jq:~L ~s~ m l;:x,=m I II I II J 15 ~s isomwau B m [~x'-'m I miK~q. ~ Y-Ix~ l~ndin ote~n m [x,m II II III III 7q~, a~,t~ch~ne,~w, m ; ;~" IIII I I I HLA-C [,x0=m I III II I m [+I*Pl [I ! ovarian ~anulou ~ !3.0kD l~olmin HGR74 m t,X,.,:.,,,,- I III IIII m l'~ '[m Illlll 4 ~:JCoA "mm m [;~,~i . II ~e a,.m oein hee d~in m [,X~l I IIII I ~_..._.,~.~ Ear of m [,x,-~m m. I(~I:[,:-7:: :::- : m~j J puta~e dbo6omal protein LI$ m t:x,~,-- IIII III III mimch ,ondri~ ~ai~inol-~loCnrm,e C redu~tHe 11kO p'o~n [,X,-'I rlbosomJ otein 1.23 m i:;X.~i I ~deoule m ~!0z IIIIIIII II '-" , 22q12.1..,R13..2 metdoprotwnase 3 inhibilor m [,x,=ml III I III I <, fe~¢ acid-lncIud~o trarlscllt~lfftirtMe homologu! m [,X,Zl III I al~ial;~;~-' II II II 11q2a.a ,~.om,~ Fot~ s~. [+X*Pl 5 sarcomeric mitochondriat ¢reelino kinase IX ~1 I tochrome C oxidme 6B n "in m [,X,[1 1~I kJco~ Var~ ter 5 m (,~,~'"- II IIIIIII I ~$~rm~ oton P21/H-Ru-I [;X,~I f m Hr,~m II II II randomly s~n~ded eDNA D1 3642 m [xiiiii~" 1i II I mll;l II 1 9ql 3.3 electron transfer flavoprote~n beta-subuni! m ~;~;~l lll;I :~r t 5q24-~5 ~ruv~te kk~aN m [,X,~l L,".~k ~nolam kleldncinLpromin [*I*[! ll|;I Ill II . .11p1..3 " catal~se [,~,~m I IIII I IIIIII ORF Mi F ~ea~ome delta chain 0.04 , 5q31-0~33 HLA-DR antigens al~c~ialed instant chin 0.04 , ,, ~al~in inNb~or O.04 4 4 STS 4-248 0.04 20 , 20 major c~om~e autoanli~len B 0.04 6 ] I'IGrFB,FLS ...... r,x~m,~ FO~,in Sa h ,~t 0.04 1 ,BR ...... 12ql.3, ,. hnRNP AI 0.04 hnRNP A2 ...... I ,,°.m , nuclear r¢~iratOr~ factor-1 0.01 ,. randomly' ~m~ed cDNA D13643 0.01 I~2 0.0t ,., P-selecSn li~,and 0.01 , randomly samF~ed cDNA 025217 0.0t 7 .. 7p13-p12 IGF binding prol~in 3 0.01 9+IO 9q~2.1 .~22.~.. ~o~in L 0.01 Sp2~.~ ,,,.~ppm~t C~ 0.01 I1[~] 4 , 1,,7q~s, ~,~.q f~to, sc~.,, 0.01 .~OO~ muscle protein 22-alpha 0.01 12.* 17 , prot~ tyro";ne kinase .... 0.01 ~. serine/b~eor~n~ptole~n kinalm re~ptc~ R5 ,, , , 0.01 coatomer beta' subunit 0.01 . deoxy~tidylate deam~ase ' 0.01 ' 2(:137.3 eolla¢je~ Vl ~pha 3 0.01 1 ' I! HI ...... ",' DNAJ protein homo~o~ 1 i 0.01 ,i 10q24 urokinase.t~oe pIMmino(jen activator 0.01 6p21.3 re~no~c acdd receptor RXR-beta : 0.01 " 9, ,91utarna~ transporter U~9 0.01 . vacuolar ATP ¢~mlha~, subunit C 0.04 : 3 i HL, PI 17p11-qm. .... ~toc, ke~etal ¢jmmma-a¢Sn 0.04 ~ ,0.03 18 I HItFBeBR~PIIPL 7p15-p12 cytoplasmic aelin 1 (beta) , , . 0:05 randomly sampled cDNA D17793

296 ~I GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

Appendix 1 B: Homolog gene transcripts

OENX % Muscle % Brain ~q Tlleues eSTS, Spe¢lea Oene product 1 0.09 Bovine mitochand~l NADH-ubiqumone o=idoreductaea49kO ~bunit 214 0.08 7 FBtBR 8 Mouse SCG10 ~ne ..... 263 0.O1 1 FLS 8 Pig 17 bete-estredloi dehydrogena'~e ,,, ,, ,,, 29/' 0.03 2 BR Mou=e t,~mium bindinq pro~n , ,, ,,,.,,, 311 0 01,, 1 BR ..... 1 I~m.,ster monocarboxylate tranqx~,-,~," 1 351 0.02. Pig,, ~m~ ~goPel~deae 352 0.53 ..... 0.01 2 ~BR,PI 1 Rat UNR protein wffh unknown funclion 358 0.01 Rat beta-alenine syn~'~se 447, O.Ol Rat.. eden~de!e cydeset ollsotwe type 3 4/3 0.05 14 FB~BR , , Rat beta lubulin T beta 15 341 0.01 7 ~BR,TE Sheep (~phosphogluconate dehydrogene=e, decarboxy(aling 851 0.10,, 5 HI,F,B,RE 5 Rat poste~apti 9 densi~ protein 95 562 0.01 1 HI Rat Prot~-tyrosine,phosphatasa striatum-erwiched ~6 0.03 1 :BR Bovine vacuolar H-ATPase subunit D 821 , , 0.02 Rat hem.2 697 0.03 3 ;BR Rat 150kd d~ein'=msocietad I~divpe~de 7=. o.o4 o.oi s mitochondrial NADH.ubiquinone midomductass 13kD B subunit 790 0.09 0.03 5 HI,BRaHE 5+22 Pig econitafm hydretase (aocnitase) 827 0.01 Rat hemin-eenmfive initation factor 2a Idnase 0.13 o.o8 1 an ,~6 Ra,bbit ..... phosphorylase kinase beta ch,aln 1078 .... 0~07 2 FB~BR Mouse membrane M6B ~169 O.Ol Mouse KYBP 1169 0.01 Bovine neurophilln 1180 ...... 0.01 , Mouse mdm-1 1222 0.01 1 ~11 , 0.01 2 HL~BR F~mstar , argin)4tRNA syn~etaas 1278 0.oi Rat , N-heparan ~ulfeta sulfotransleraea 1290 ,,., 0.01 Mouse. can trocyclin 1296 0.05 ,7 BR Mouse serum inducible kinase SNK 1367 0.01 Mouse brain Protein 147 (fragment I 1455 0.01 Rat .qlutamate receptor subunit GIuR6 1527 0.01 Chicken , , probable G protein-eoupied recep~ ,8,HI 1577 0.03, 'i BR Rat...... cytopl~micdynein 74kd interm ,ediate chain 1502 o.03 1 BR ...... Rabbit cardiac ryenodkle receptor 1610 0.02,,. ~ ...... Rat , , , Ion~-chain.fattyTacid.coA i.qaeabra'in isozyrne 1805 0.01 1 BR Duck maters oxidoreductase 1817 0.01 Rat chloride channel protein 2 1855 o.01 3 BR Bovine , 'gamma.COP 1873 0.01 2 BR Rat..... syntexin A 1874 o.o1,, 1 ,I BR Rat ! L:er ginine:glycineam idinotr ansfar ass 1878 0,01 1 ! FB ' " Rat i insulin-induced ~owth response protein 1899 0.01 Rat ,,, brain sodium dependent glutamatelsspartate transporter 1914 0.01 2 BR~,CC Rabbit lam bda-ctysta.llin , ,, 1915 0.01 1 HL Mouse H beta 58 1~.8 0.02 1 Bn .... Rat NMDA receptor giutam',te'binding subunit ..... 1943 0.01 I BR Rat protein phosphatace inhibitor t 2024 0.04 0.01 I BR Rat I histone H2A.1 2028 0.01 Do<:j Rabl 0 20¢1 0.01 1 BR Boyine i inorganic 2049 0.02 6 HL~BR~FB Rat cytoplasmic heavy chain 2385 ,,, 0.01 Rat CaBP1 ¢~ciu m binding protein 2129 0.01 Bovine ~phosphatidylinositd 3-kinase requlatory beta 'aubunit' 2148 .... 0.01 1 FB I Mouse T-celt an~gen receptor alpha chain 2177 0.03 ! Mouse , NDPP-1 2302 0.01 Mouse putative GTP-binding Protein Movl0 2~ I O.Ol Rat glycogen synthasekinase:3 beta 2346 0.03 4. HL.BRrHA Mouse ; br~n protein E46 2386 0.01 Mouse i novel beta 1-4 galactce~transforase 2386 0.01 1 FB Mouse ; glutamate (NMDA) tecepto¢ subunit epsilon 1 2401 0.02 1 BR Rat !, ,qam ma-aminobutyrk:: acid tr anspor tar 2434, O.01 2 BR Rat brain specific Na+-dependent inorganic phosphatocotranspor tar 2462 0.01 , 3 FB BR Mouse amytoid-like protein 1 2473 0.01 1 BR Rat f.spondin 2480 0.01 Mouse serotonin receptor 5HT7 2546 0.04 0,01 ,, I BR Bovine , cAMP-regulated phosphoprotei..n.(ARPP-19) 2558 0.06 7 BR~FBTBC Bovine i p87 transporte~-Iike protein 2684 , 0.01 Mouse ; serine/threonine kinase leak-a) 2708 0.01 Bovine chlorine channel P64 271i 0.01 Bovine NAD+-deloendent isocit'ate dehydrocjenase 2740 0.01 Rat ...... major vault protein 2749 0.01 2 FLSrBR Mouse NGF-inducible protein TIS21 2~4 0.01 Rat aynsptota~min 3 2813 0.02 ~,1 BR Dog mucin,, 2822 0.01 Mou,. :: mesoderm.specific uqk~ pr,ota~,,'" ,i" 2844 0.01 Bo,,ine ! ectin-like protein 2899, ,, 0.01 Mouse ARP-1 (COUP family of nuclear orphan receptors) 2917 0.04 0.02 9 FB,HI~BR Rat 114-3.3 protein epuilon 2920 0,02 3 BR Mouse RNA/DNA binding protein RNPS1 299o 0:04 I 0.01 1 HA Bovine mitochandrial nicot~namide nudeotide transhydrogenaSe 2992 ' [ 0.03 ..... Rat voltage-gated potassium channel 3087 0,02 Rat i ~dium channel protein I 3111 0,29 15 BR;PI Rat neulonal olfaclomedin-reiated ER localized protein 3131 0.02 Rat ...... potass',.Jm channel KShlIIA 3!40 0.03 1 BR D~ Ra~2 3152 0.13 0.02 5 FB~HI Rat ; 14-3-3 protein gamma ...... 3155 0.03 !Rat 100kDa protein 3173 0.02 '1 HL qhicken .. o~ein licjht d,,'t,ain A 3193 0.03 Mouse invasion inducing protein Tiara-1 3220 0.05 4 HLrFB~PItBR Rat translation ini~ation factor 5 3221 0.03 Rat vesicle associated membrane protein VAMP-2 ' 3279 0.04 0.02 1 FB Rat i nuclear factor 1 3287 0.02 I HL ,, Mouse glucopaminyl N-deacetylese/,.,,N-sulfotransforase 3357 0.09 0.01,, 2 HLrBR 1 Rat ~roteasome RN3 subunit 34OO 0.O7 1 FB 19 Rat i glycogen syntase kinase-3 ¢~s ...... 3403 0.07 1 BR 19 Mouse synapse specific phosphoprotein F1.20 3412 0.04 0.01 3 Sov~e mitochondrial NADH-ubiquinone oxidoreductase SGDH subunit 3422 0.26 2 HL~PI 2 Mouse hnRNP X 3429 ;0.18 6 Rabbit ...... junctional samop~esrnic retioJlUm glyceprotein (triadin) 3455 0.04 0.01 1+10 Dog ~gnal rsoognition parade 9 protein {SRPg) .... ,:~0 o.o~ 14 !Bovine mitochondrial ATP synthase coupling factor B 3477 0.18 Rabbit skeletal mus,de myosin regulatory light chain 2 type 2 3487 0.09 2 HA i Bovine mitochondrial NADH-ubiquinone oxidoreductase MLRQ subun!t 3490 0.04 0.Ol 2 BR Bovine mitochondrial NADH-ubiquinon,e oxidoreductase 51 kD subunit 3501 0.04 2 i HG , x~nopus ribosomal protein $27 homdogue 3528 0.13 2 [ HL,TH 8 Rat ribosomal protein L30 3549 0.13 1 RaU,it skeletal muscle calsequsstrin 3582 0.04 0.01 1 HG 2 Mouse differentially expressed homolog of HepG2

297 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

Appendix 1B: Homolog gene transcripts (continued)

3570 0.09 .... Rat fast ~eietat muscle trop,on~, in T ...... 3585 0.09 0.01 2 TE 2 Xenppus double stranded RNA bindincj prctLein ,A 362O 0.O4 5+7 Bovine mitochondr,tel NADH-ubi~none oxidoreductase '822 subunit =1647 0.09 Rat n ,eonetal,calcium ATPase ...... ,, 0.02 t BR ,,, , ,~ , Mouse morpho~oni¢ protein Fil 3715 0.02 20 ~wine 1 -phos~haddvSnositol 4,5-biphosDhata l~pho(~esterase beta I 372O 0,08 ~.., HI,FB, ,B,R, g Bovine .... UNC18 ~eo~ .... 3723 0.03 r8 BR Rat mteojese.like FE65 .....3 TM 0.02 , i-~ Rat TRAP.,oompex 9arnms subunit 3/'37 0,02 Mou~e • potauk,~m channel eubunit (m-ug) 3751 0.02 ;Bovine n~=Jrexin III beta 38O4 ,, ,, 0.02 , , 12 Rat initiation lector Elf-2 =?6 ,, 0.02 4 Rat c#lmoddin-de,pendent prq~,in kinace 2 de,its 39OO 0.03 I' " FB Mouse membrane glycoprcteln M6-A 3942 0.09 0.0~ 4 H!~BR 7 Pi~ mitochondrial malete dehydrogene= 3954 0.02 Rat Opio~d binclng protein / cell edhe~on molecule 3O56 ,, ,,,.... 0~02 10 i ...... Mouse SDF-I -bets ...... 3~0 O.OG [ 2 HG,BR 2 Rat ~sinin4ike Protein 1 0o5 Rat b~-ooat Protein i.4116 0.04 0.03 I , OR 2 Pig cyto~a~ic malete dchydrogenase 4183 , 0.02 1 Rat Rab, geran~igorenyt Wnsf~ese beta subunit 4198 0.02 ...... Ret inten=on related put.re p'om~ ...... 4217 0.,02 1 P!,,, Mouee Rab.I8 423O 0.02 Bovine muil]ub~ultinating enzyme 4236 ..... 0.02 '4" HG+HL~BR ,, , " Rat DNA bindin 9 protein URE.B1 4=. 0.03 M,ouse Prcteln-~osine phusphataSe kappa 4=74 0.02 Mouse enhance.trap-locus 1 .,,4,296 0.04 0.01 2 HE Rat protein pho~ohatese I catalpc subunlt , ,, 4295 0,02 3 BR Mouse, inositol 1 ~4~5-triphosphste-binding protein type 1 receptor , m 43O3 O.O4 ,, Rat ribosomal protein [.3 i 4340 0.05 1 BR Bovine , epellon-COP 4368 0.02 3 HliBR Rat syn taxin B 4371 0.04 0.02 Rat )gophyrin 4294 0.02 1 BR Rat mitochondriel ~lycerd-3-F~nosphatadehydrngenase 4308 0,04 0.02 7 FIG Mouse I TNF, r,ec.eptor re!ate d protein .... 4450 0.04 Mouse syn~ophin-2 ...... 0.02 Rat ...... potassiu m channel , , 4473 0.09 Rabbit i sarcoplas..m!creScu!um calcium ATPase laSt twitch ~eletd mqsde 43o2 0.04 Rabbit .... glycogen-associated protein phosphatase,r,egula,tory 4ubunit 4S21 0.04 Rat gam,ma-glutam)4cystelne synCs,tess light subunit , , , 4538 0.04 Rat baSk: transcription element binding protein, [] 4600 0.13 4, HGfHA 14 Chicken ~oStin 4648 0.04 8 Rat extraceluler signal re~julated kinese 3 (ERK3 I 4670 0.04 ,,2 Mouse ,, putative Calcium binding protein MO25 4,?47 0.04 Rat putaSve ,cal,cium pump _ 47"/6 0.04 10 Chicken inte~rin eiphs 8 4m2 0.04 ml[:] 20 Mouse RNA-binding protein 48OO ,, , o.01 Rat neurexin 4as~ 0.oi 2" HI',RE ..... Rst ¢ kinase scbstrete celmodulin-binding protein RC3 4928 o.o!, Rat metabotropic glutamate receptor 3 4973 0,0t 3 BR Bovine leukemia virus cell receptor 5OO8 0.01 Bovine poly(A) polymerase 5O33 0.02 2 FB,BR Chicken NR-CAM cell adhesion mde~le 5O87 0.01 Rabbit endopepddase 5157 001 I Rat transcripSon factor RZR-beta 5171 001 1 HI 17 Rat , , da~in-coated,veside/spa~¢ veside pro,~n pump 116kd subunh .., 51B6 0.01 Mouse protein overexprassed in IIsticut~r tumors ' 5188 I 0.01 Do9 lm¢61 he,m,alogue , 0.01 17 Mouse B6D2F1 done 2A-1 5~7 0.01 14 Rat ,, Rab gerenylgeranyt transferees alpha subunit 5~1 0,01 I BR Rat metabotropic glutamate receptor 2 S~O o.01 3 Rat =odium and chloride.dependent GABA transporter ,3 o.o!. Rabbit bleomycin h~Volese 5326 o.m +, ~,CM,BR , 9 Mouse surfeit 4 Protein ~76 ,, 0.01 2 BR 11 Mouse flap endonudease-1 547O O.01 1 BR Bovine pyruvste dehvdroqensse (lipoamide) phosphatase ,., ss~s,...... 0.01 1 BR Bovine neurocetcin 5580 0.01 "6 Mouse ribosomal protein $6 kina~ II alpha I 5574 0.01 11 Rat LI.5 5578 o.oi Rat 3-me~yl 2'.oxobutanoate dehyd'rnganaas (lipoami,de) kin'-se 577S 0.01 3 Rat I integral membrane glycopr,ot,elnGP210 .... 5927 002 3 HI~BR ,, Bovine 596O 0,01 Picj ,,, I protein P97, 6075 0#4 75 Mouse ZFP29 §077 0,04 2 ,, HI~TE 1 Hamster mevalonate b'ansportar 6170 0.04 2 HL~FB .... 6173 0.04 2 HG,,HL , [.~'J]l! ~ I'~'~'~.J'J~ II~ P';I[eJ = ~llrl*: [. :l]iIT .: ,[:I .):4:* ~J'~'~-+ +[I];~. ~= +:'+:]I "J l~-~+J.~+Jtr'~~ 6174 0.04 I PIG r:~cf ubiquind.cytochrome,C reductase subunit, , , 6193 0.09 I BR 3 Rat dethrin cost assemb~'t' protein APS0 6257 0.09 , , 22 Rot da~rin heavy chgin 6280 0.04 Rabbit cytoFdasmic glycerd.3-phosphst?, Cehydrnganass .... 6293 0.04 Rat,, V-1 Protein 6310 0.04 Bovine mitochondrial adenylate kinqse 2A 6317 0.04 6 HGrFB 5+16+20 Mouse ribosomal protein L27A 5318 0,04 1 TH ' Rat ribosomal protein L11 6321 0.04 Mouse single strand DNA bin~glprotein P9 6332 0.04 Rat da6"vin associamndprotein P17 (AP171 5338 0.04 ,,,, ,, , 1 CM lZ Bovine mitochonddei ATP s~thaee D chain 8349 0.04 I prey end,opepS,dase , ,, 0,04 2 Pl Rabl 4 6361 0.04 5+7 ~wine )retain kinase C inhibitor 1 (PKCI-1 6405 0.04 [ Do~ chloride channel 6424 0,04 3 , FB PI~FA Mouse interleukin 10 (ILl'O i ' 0479 0.04 1 I HL Bovine mitochondrlel NADH-ubiquinone oxidoreductase 14.5kD A subunit 6S31 0.04 1 i HG 17 Bovine mitochondrisl NADH-ubiquinone oxidoreducts~e 15kD subunit 6555 0,04 Mouse nedd-l,, pr~eln 6582 0,04 15 Rat 9uenidinoacetate N-methyIrenrJerase I ,6587,,. 0.04 ,, 1 F B 3 Rat ribosomal protein 1=8 66O4 0.04 17 Rat myosin I heavy chain 6508 0.04 5 Rat edentate ot,dase type 2 6629 0.04 Mouse TIS7 6649 0,04 Mouse EVI.I 6659 ' 0.01 Rat protein kinase C regulated chloride channel 5669 0.01 ,, 3 BR Rat o/steine.rich protein 2 ...... 6603 0.01 Mouse kineain-like protein KIF2 6713 0.01 Rat, ¢alcium/calmoduSn-deFendent protein kinase type 2 alpha , 6773 O.Oi 1 'BR Rat plasma membrane calcium ATPsse brain isoform 2 67a0 0,01 Uo~

298 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

Appendix 1C: Related gene transcripts

GENX % Mu~e % Brlln Sec "nNu~n,e eaTS Mlp Spedes ~product ,~ 22 0,01 9 'Yeut GTP-binding protein GTR1 27 0.04, 0.01 1 HL 1 . ~..,2.qt3.31.qw Human NADH.c~ochrome B5 teducteae 41 0.01 2 BR ;C..elagans i h~theticel 152.4kd,poll~n ZK3,70.4 in chromosome III 64 0.01 E. o~..i...... ; Ail-tRNA-la 01 0.01 , 11q!1 Human ox~ste~d-bindlng protein ?s 0.02 mmI Human ~'msfor,,ming protein RFP Tt 0.01 ,. 12 Human ur~I-DNA gl~ce~lase 1 78 0.01 ,2,~.3 Human cAM P-reSisted mRNA 1 08 °.°! ...... 5 Mouse : me,fief 2 Prom~,, 112 ..... 0,01 ~ 12 Mouse : natural re~dstance llseO¢iatad maerophage p'oW!n 122 0.01 5 4q26 , Human microanmal UDP-glu©uronol,/tl;anslereae 2B7 125 0.02 Pig .. isc

299 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Appendix 1C: Related gene transcripts (continued)

1190 0.01 yeast serine-rich RNA pchtmerm I supprasse¢ 1227 0.03 '1'q32.1 !Human MAP kinasephosphatase I 1233 0.01 ID~osophilie , cadherin-mlsted tumot suppressor" I'~otein FAT ~ ,, 1244 0~01 I H~ Xp11 2~-=m Human 9astrin-releesin9pep'ade recep~ 1248 0.02 Ple~odon I WNT.IOB protgin i270 0.05 3 HL/B'R,FB,' 'I1+19 ...... Mouse sub=ote..o! protein t~rosirm kinase'reoaptcrs end p6Ov-¢4"c 1276 ,, , 0.01 ..... Human focal adh ,e~on kinaae 1305 0.0t 2 HLrFB Do~ , ,, g~,coprote~ 2.5L 1306 0.01 I HA 21 Human I zinc fin~ler domains ZF21.3 1320 0.01 Bovine cartilage Isucine rich protein 1324 0,03 Yeast YME1 1326 00t I Ft Chicken sodium potassium transporting ATPase beta 2 1336 0.03 ,,,, , , D~o~oph~, darer seqregationa~ protein 1~6 o.01 3 F.B,pi.,CC Tobac=o ~oradoxin 1364 0.01 ,,,, ,, .~hicken ..... probalde G prp~n.ooupied receptor 6H1 .... ?~7 o.oi 4 CM,BR~BC , ,, Mouse nicotine acetyIcho~ne receptor beta subunit 9ene 1412 0.02 2 i FBtBR C. e~.9ans hypothelical 54.9 kd Protein CCY2FS.7 1418 0.03 tp13 Human CD53 1~ ,0.02 P~9 inhibin beta, e-subunit 1448 0.02 ,, Dt0~philie white protein 1507 0.,01 , , DO(,] cytochrome P450 2B 1536 0.01 1 HA Yeast phan~4ala..r.~!-~NA,,eyn~etase alpha ¢hain,c~plaemic . , 1~7 ~ o.01 ,2 BR Yeast hypothelical 75.5kd protein in SDH1 -CIMS/Y'rA3 intergenic 1573 0.01 Human zinc firmer protein 7 1579 O.0S ,, 21 Amoeba myosin heavy chain IB ?ms 0.o~ 0.os 4 HL,FB~FArHA 20 ...... Rat 14-3-3 protein beta 1616 0.02 I BR Human DNAJ protein homolocj 1 1635 0.01 , , Yeast tRNA isopentenyItrens far ass 1662 0.01 13ql 3 Human caseine kinase 1 1672 0.01 1 BR ,, Rat ecTI-pepti..d~.,,.hydr ol ,a ,se 1678 O01 Rat TR4 orphan receptor (steroid receptor1 ' 1693 0.01 Drosophilia cadherin-related tumor suppressor protein FAT !~ o,oi Yeast tRNA-splicing endooudease positive effector 11~8 0~01 6p21.1-pll.2 Human er~, roc~.e.,ankp'in, 1700 0.01 2 BRTFB Human splicing fa~.t=Or CC,1, ;3 1~7 0.01 2 BR Xenopus gastrula zinc linger protein"XLCGF5~.1 ' ' 1721 0.03 t BR Drosophitia casein kinase 2 t alpha ch,aln 1743 0.01 ,,, Yeast hypothelica134.9 kd protein in URA1 1767 0.01 Human heat shock,,!actor (HSF 11 1779 0,01 C. elegans putative ATP.dependent RNA K03H1,2 in chromosome III 1791 0.01 Dictycateiium deveiopmentally re,~,a!ed protein lunase 1 ..... 1916 0:04 0.03 16 Mouse ta~292 1827 0.02 22 C, elegans hypothedc,,a,I52.7kd protein T2395.2 in chromosome III 1842 0.01 1 BR Mouse GABA transporter ,1856 0.02 Droecphilia serine/threonine kinase Fused' 1860 0.03 1 BR 17 C. elegans hypothelic~ 52.7kd protein T2395,.2 in chromosome Ill 1867 o.01 I CM Human zinc fincjer ZNF139 1983 0.01 Rat .quanine nudeotide releasing protein Pt 40 Ras-GRF 1908 0.02 Xq21.33-q22 Human t~Kosine-protein kinase a~, 1912 0,.01 Xenopus ribosomal protein $6 kinase II beta 1929 0,01 Rat skeletal muscle myosin light chain kinase" 1947 0.02 1 BR Yea,st BCS1 protein 1~7 0.oi 1 BR Yeast zinc flncjer protein GCS1 1965 0,04 0.Ol 5 HLrBR 1 Chicken ribosomal protein $6 kinase II alpha 1974 0,01 3 FBfPI.HA Rat addudn-like 1978 , ,, 0.0t C, efagans, hypothel~cal 87,6kd, Protein ZK637,.3 in chromosome III 1996 0.02 Ipt3.1 Human 3-bets hydroxy-5-ene st~.oid dehydrogenese type II 2042 0.03 5 H!,BR 19 Vaccinia virus protein K 4 2047 0,02 2 HLjBR Yeast leuc~ne-tRNA s~mthetase 2068 0.01 Vaccinia virus protein K4 2078 .0.01 Mouse guanine nudeotide releasing protein P140.1~, s.GRF 2000 0.01 4 HL,BR B. sublilia ini.tiation factor IF2, 21o6 0.o~, 3 HGrBR Bovine CSSM015 microsateltite 2138 0.01 Rat neuraxin 2140 o.oi 3p21 -I)22, Human transcription factor ..... 2158 0.01 I BR , , Neurcapora sulfate Pormeaso II 2162 0.01 S. pompe CDC5 ,2172 0.01 1 BR C. elecjans putative ATP-dependent RNA helicase T26GI0.1 in chromosome III 2174 0.01 Xenopus oocyte zinc.finger protein XLCOF26 2182 0.01 1 BR' Thermus e. succin),l-CoA spthetase beta chain 2188 0.01 Rat cjuanine nudeotide releasina protein P140 Ras-GRF 2194 0.01 Yeast SCO1- 22O9 0.01 17q21.3 Human MDC protein '~ 2226 0.01 1 Human HKR,3IFo ~ 2228 0.01 ! CM/BR H, marismortui 30S ribosomal protein HS6 2238 0.01 Kfabeiells terr. ecetdaotafa s~lm~ase 2,~so o.ol 3q22-q25 Human pdpden),lata binding protein 2254 0.01 2 BR ,, V=osinia virus hypothelcal 5.3kd protein 22e3 0.02 I BR Cryptococcus n. ADp ri~syletim fa,c~ 2267 0,01 Mouse ECA39 2297 0.01 12p13 Human 91ycerak:lehyde 3-phosphors dehydrogenase 2m8 o.oi Human myelin transcription factor 1 2341 01,01 Chicken cartilage matrix protein 2345 0.02 .., Human erythroc).te band 7 integral membrane 2362 0.05 5 Drosophilia ubiquitin-conjugalin9 enzyme E2-16 kD 2380 0.01 X Movse brain ,protein DN38 ...... 2306 0.01 Chicken , epthelial-cadherin 2308 0~01 19 Yeast 32.3kd protein in APE1,LAP4-MBR.1. intergenic region 24O3 0.01 Human PGB4G7 ,qene 24O5 o.01 I HE X Yeast transcriptional regulator), protein RPD3 .... 2413 0.01 3 BRrCC 7,-11 Human DNAJ protein hornolog I-roJ1 2423 0.01 Drosophilia suppressor of forked protein 2453 0,01 Human CMRF35 2477 0.01 1 CM 14 6<:122.3-(:123.1 Human erpasa 2478 0.18 0,05 1, Human dual specificity phosphatase tyrosine/serine 2~o o,01 Chicken lamin B 2504 0.0t I HL Yeast hypothetcd 195.2 kd protein in GCN3.DAI'80 2513 0,01 Yeast hypothe~cd 45.6kd protein in TPD3 3' re,on 2614 o.0t =, , IC, efagans h~tpothe~cd 50.4kd protein ZK637.1 in chromosome III 2520 o.01 179 Human tre oncoqene (deubiquilinase) 2550 0.01 2 BR !Dictyosteiium, coronin 2556 0,03 3 FBfBR ISalmonalla t. protaase DO 2~2 i 0.02 1 BR IAmoeba myosin ,Ic hew)' chain 2566 0.03 12 !Mouse ooc~e maturation OM-1 300 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Appendix 1C: Related gene transcripts (continued) 2r~6 0.01 Arabidopsis qh. oeil 0%i~' coned protein 2 homolog A 2571, 0.01 Human r~,K~n, ai protein $6 kinase _~s78 0.03 2, BR 7 [~oacp~I,, s~it Prot~ ....2380 0.01 1 HA ,., ! ,, , ,,, Rat .R~acto~-speci~cle~n .. 2388 0.02 4 HI=BR , , 5 :1610 0.01 Mouse ZFP26 2620 O.01 i, , BovmeYeast " ' ~hlorine~enereirN~al~Veehan~l P64're~' ator ol ~-enacripl~on subunit 2 (NOT2~ , ,,, 2627 0.04 0.01 1+9 I

=m o.o,I 1 BR Ypt 1,3 Human zin~-finger Y-oh,remosomal Protein , "1 2631 0.01 ;1038 0.02 "/' TC,FB:BR Xq26.3-o,27, I Human proto-oncogene dbl 2642 0.01 2 BR C. eke,,ana hypothelicd 152.4kdprotein ZK370,,4 in ,chromosome III, 2M6, ,, 0.01 Bovine mitochondds! ni,octinamide nudeati ,tie trw,~,shydtogenase :m~ o,o2 Human ,. liver cytochrome C oxidase 7A 2662 0.01 3', HL:FB~BR Bovineleukemia virus ga9 polyprotein 2/03 0.02 i p22.1 .qt=, Human auto, pate dehyckocjenase lubiquinone) hvopr'otein t~Jbunit ~, o.o4, 2 ~31~132 Human nebulin 278? , o,01 Chlsm~onea t. ADP-ATP trandocaea 2784 0.03 ~ TH,H~,~e Yeut Pro~ebl!pid protein PPA1 2?96 0.03 ,~,, ~eR C, ele9ans ..... hypo~e6od 25.9kd pro,rein C05B5.7 in chromosome I1! 2810 0.01 ,I0~2,3-~4 , Human interferon indu¢,ed protein 56kd ,,, 2863 0.01 1, !BR Yeast transcriptional regul,,atorY protein RI~'D3 28135 0.01 Human teiomere asso<:ialm~ repeat UCl~Jence 28119 0.01 1 HI 17 Hum,an , I~roline-S-cetboxylate reductase ., 2Be6 0.01 Mouse parlorin ...... 2g05 o.01 12con-q21 Human ~fnsptote~min ,1 2910 0.01 ! BR Trichoderma r~, eiongation lac~r I elF:ha 2930 0.01 Yeast , pre..mRNA sp~icin9 facto- RNA helicase PRP28 z~ .... o.0~ ..... Rat ...... paroxiaom,el enpyl hp~'at.e4,ike ..... 2947 0.01 ,,,,, , . 16p13.1 Human GST1 -HS GTP-bindin¢j Protein Z=Sl ...... o.oi Yeast dathrin associated Protein AP17 2963 0.02 4 pIrBR,HE , ! 0q23-q25 Human inauGn-decjradatincj enzyme , , 2977...... 0.03 Mouse synsptotagmin 4 28e3 0,02 5 HL~BR~FB~,BC ...... 19 ,6,p12 Human .... hnRNP G, , ...... 3oo3 0.03 Mouse potassium channd mShel 3008 0.02 4 HIrBR Mouse FKSO6-bindng protein ,, ,, 3022 0.03 2 BR C, eiegans h,fpothe~cal 63,5kd Protein ZK353.1 in chromosome 3 ,, 3027 0.06 Xenopus omithina decartx)x)4ase 3036, 0.03 6p21.3 Human , , HLA d=s,.s,-2 66kb-re~ion ...... 3041 0.04 ...... Chicken smooth muscle m)~asin light chain kinase ...... 3050 oo2 , Human peptidylproline cis-b'ans isom,erase A ,,, :msa 0.o~ Rat putative zinc finger protein 3068 0.03 II :bl.~m Rat calbindin D28 ,, 3103 0.02 C. ele,qans I ubic|uitin-conjucja~n 9 enzyme E2-17 KD 3116 0.02 Human ribosom d protein homologous to ),east,S24 , , 3119 0,09, 0.03 3 Pt~BR X+9+16 Rat MAP-1A and IB li.qht chain 3 3121 0,02 1 BR Mouse gamma adeptln ,, 312,2 0.40 0.02 1 BR ...... X+3 1 q,2,4,:q32, Human ,,, cyst,,ein-ri,d'l protei?. 3159 0.02 1 BR I p22.1-citer ' 'l Human , ,, succinate dehydrogenase (ul~'guin,one) flavoprotein subunit 3169 0.02 E. coil sigma cross-reacting protein 27A 3172 0;02 1 19 Human HKR1 3186 ,, ,~ 0.03 Duck malate oxido~eductase 318~ ,,O~03...... 2 BR 1p36:p31.2 Human guanine nudeotide.bindin~ protein G(il/G(,s}/,GIt ) ,beta subunit 1 3239 0.02 ,,, 4q25-q27 Human b~ain ank~in , 3249 0.02 6 1 p34.2-p3,3 Human , er~hroid pro,tain 4,1, .... 3282 0.07 4 SR,CC,I:I~" C. eie,qans hypothe~cal 80.7 kd protein ZC84.3 329~ 0.04 0.03 2 HL~HI Anacystis nidutans elonqation lector Tu , , 3~o2 0.o4 ...... 1 ..... 11 ql 3-cL14 Human skeletal muscle alpha3-actinin 33qp 0.03 1 SR .... Human , putative centromeric DNA ...... 3313 0~03 Yeast elongation factor 3 3326 0.02 Rabbit phosphoglucomutase isoform 2 3334 0.02 '1 P'I Human HSP47 3370 0,02 2 BR~CC, 7 ...... 7q21-q22 Human serum paraox, onase/ary4esterase ...... 3384 0.26 2q31 -q32 , Human titin 3~ 0.02 1 H L C. elngans meiotic spind,e for,,m,ation protein MEI-1 0,02 2 TE Human heat shock 70kD protein HSP70RY ,3442 '0.13 17 17ptar-p11 Human skeletai .,musde beta-myosin,heavy chain 3443 0.04 X+2 Rat hexokinase 2 3449 0.09 1 1 q24-q32 Human oys.tein~ich protein ~3 q.~ 1 cc Human heat shock protein HSP27 ~'~ ,, 0.~ 22ql 3, Human interleuldn-2 receptor b,eta chain ...... 3486 0.09 ~7 17ptar-p11 Human skeletal muscle beta-myoein heavy chain 33o~ 0.00 17ptar.p12 Human parinatat cardiac myosin heavy chain .... 3517 0.09 2 HL,CC 1 Mouse MSP23 mRNA 3531 0.09 ...... 4 13 Human relnobleatoma su ,spec~bility 9erie 3533 0,04 o.01, , 14 Dianthus c. , glutathior!e S-tranaferase 2 3536 0.26 10 2q35 Human , villin 3539 0,31 Rabbit titin 3545 0.04 3. subtJlis 91utamyI.tRNA ayn'thetase 3~a~ 0.13 Xq28 Human non-muscle filamin 3~s 00~ 2 Rabbit titin 3604 0.09 8+9+15 Bovine milocho~dr~.l ad~yla,, ki;;:'se ~...... 3616 0.04 t9 Xp11.3-p11,23 Human ZNF81 3644 0.09 ,,2 Rabbit titin 3653 0.09 / 3 6p21':3 " Human HLA class-2 66kb-re¢jion ' " 3668 0,02 3 BR ...... Rat , protein pho,s~atase 2S catalytic sut>u~t I 3684 0.02 5 , HL~HI~BR Yeast probable peroxisoma! tarcjeting signal receptor 37O4 0'02 4 FB,BR Xenopus proto-oncocjene t~,osin? protein kinase Yes 3.n.1 0.02 2 BR 17 16 Human carbonic anhydrase 5 3756 0~04 Dcasophilia sererKtpi~ locus protein H.1 3767 ~o~ 19<]13:1 Human zinc finger ,ZFP-36 3781 0.02 19pi 3.1 -pl 2 Human zinc finger protein ZNF91 .3784 0.o9 Bovine., mitochondrial edenylate kinase, 3 3785 0.02 , 3 ,, , Rat , , MRC ox-2 anligeae 3786 0.03 ...... 3 Yeast DNA repai r Protein P~, .D5 ...... 3798 0.22 2 HE 2q31 -q32 Hum ,a,n,, nebulin 38O0 0.02 2 BR 1 Bovine auxilin , .... 3843 0,05 3 HL~BR 1+3+14 Clcetridium e. DNAJ protein , , a~ , g0~ 7 Bombyx mori glycyl-tRNA Sp~le~ ~ .... 387~ 0.02 10 .... C, ele(jans hypothe~¢d 68.7kd protein ZK757,1 in chromosome ill ~L, 0.02 2 FB 20 Mouse ETO (putative transcription factor) ~6 ,0,02 ...... C. elngans hypothe~cd 46;4kd protein T16H12.5 in chromosome Ifl 3902 0,04 0.03 6 CM~HIrBR 16,,, Yeast nuclear, transport protein NIP1 ...... 3910 .0.02 1 FB 10 Drasophilia lethai(1 )dsca large-1 tumor supp'easer 301 Appendix 1C:Downloaded Related genefrom transcriptsgenome.cshlp.org (continued) on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

3~17 ,,, 0m02 12 ~.2 .~35.. Human ~lMn ,, 3~2a 0.02 4 HL~BR~FLS 11 Mouse radlxin =1841 0.02 2 FB Human membrane metelloen~dsoe 3=161 0.02 9 HI~BRrFB Mouse emyloid.like protein 1 =S,3,,, o,.o~ Mouse alpha-m sonosidase 2 .... 3980 0.02 Rat prdine-rich protein 3411~5 0.04 0.01 ...... 19 ,, 1~6.~-p~.2' ,, Human pocollagen-lysine 2-oxogluterate 5-6oxy~en~se 4o02 0.02 7 Bn ,, 7 ~se Ca++/calmodufin dependpnt protein kinase' 2 , 4OO3 0.03 , Human TALLA-1 4016 0.O3 2 BR Uou~ t~j267 4026 0-02 2p~3.q~t Human dipel~! peptiC+ 4 .... 4O45 ,, 0,02 I~13.a Human glandular, k~!~,ein 2 4O47 0;02 .... I HL 1,5, Yeast 60S fibo~,o~, ~ protein L30A',(RP29) 4O83 0.03 1 FIG Human Irmsori~on lictor BTF3b ,,,4o84 0.04 0101 , , , ,, 17 Ch.e. endol~a~min 40~0 , ,, 0.02 , Human Pr~ p~.~otese 2c "~a 4o82 0,02 1 FB Rat cytoplasmic d~n 74kd intermediate chain 4093 0,04 0.02 14 M~=, MSEC66 4 ol~ 0,03 8 HI~BR 11, MO.~ sodlum/potesaium-b'ancportin~ ATPase gamma chain , 0;.05 3 HIrBR,HA 7 Chicken emphiphl~dn (w/napic vemde-assodeted,prot~) , 4120 o.o2 ,, I HA 9 Rat, poetspaplo d~li~, protein 95 4129 0.03 3 HLrBR,cc I ' 1'8 eU~iq mala~ potentially/proteclive 63 kd anligen 4131 0.03 12 Rat sod,Jm-dependem neuroeranlmiltor Iransporter _~136 0.03 C. elegane hy1:)othplica129,0kd Prote~n ZK632.12 in chromosome I!1 ...... ,4142 ,0.02 X Chicken basic-leudnezipper4ike protein ,, 4168 0.03 1 HL ,, Mouse zinc llnger protln MFG3 4!~o ...... 0,02 Yeast nl,mlear Protein SNF4 4171 0.02 Human zinc linger protein ZNF132 ..... 4176 0.02 1 BR +Candda albicens carboxypepdidase Y 4181 0.04 0.0i 1 H E 2~t t.2 ,, Human pp60-cSrc 42O3 0.02 Mouse GABA ~ansporter (GAT41 ..... 4214 0.02 19 , Human zinc firmer ZNF 128 4280 0.02 Mouse serine/threonine-protein kinase TIK 4283 0.02 5 Sheep , ovis aries seoretory protein 4312 0.02 1 BR Rat neuronal protein P25 43,~ 0,03 I0 Yeast probable ATP-dependent RNA helicase 4337 ,0.05 3 ,HI~BR Rat a~nmn 4342 0.02 2 BR 14" Yeast FUN20 4344 0.04 6p21.3 Hu,man HLA class-2 66kb.region 4381 , , 0~04 0.03 12+17 Manduce sexte vacuolar ATP ~nthase 14ko =ubunit 43B6 0.02 Drosophilia cedherin-related tumor Ibppreasor Pro~n, FAT 44oo 0.03 2 BRiPl 1 Mouse mRNA clone pMAT1 for new ~'anafofmin 2 gene 4436 0.04 0.01 3 Yeast mitochondrial carrier protein YMC1 4445 0.02 I BR ,,, 15 Yeset hypo~elcal 21 .gkD protein in MRPL6 5' region 4484 , 0.04 2 Rabbit titin 44aa 0.04 Entorococcus h. sodbm-proton antiporter 0.o4 14 E. (eli ATP-depondent RNA hdicase SRMB 4507 0.57 2 Drosophilia ring oand protein KETCH 4520 0.04 1 Mouse transcriptional control elonlent 4542 ,, 0.04 1 HL 1 Mouse DLA.91 mRNA 4662 o.04 X 13c~34 Human NAD+ ADP rib'os~4transle;a'r,e'l)almJdo,qlm'e 4565 0.04 2q31-q32 Human nebulin 4568 0.04 11gll Human , ,, oxyaterd-bindin9 protein 4668 o.o,,~ Human TPA-inducible,c54 m RNA 4587 0.04 D,osop~m, trithorox 4eo3 0.04 Human putative Nrine~reonine protein kineae p78 4617 0.04 • I:~ Human ~toeolio alanine aminotron.sbrase ...... 4621 0.04 O. elegan+ oo=mid C50C3 ,,,4~ 0.04 9q~ Human tropomodulin 4638 0.04 2 S. pompe protein kinase BYR2 ' 4651 0.09 1+5 Yeast chromosome 5 r',Rht arm sequmce proximal to GLc7 , 4652 , 0.04 7 I~113.1 Human zinc §ncler ZFP-36 4655 0.04 i 2q31 -<:132 Human nebulin 4668 0.04 Rat celmodulin-dependent protein kinase 2 delta ,, 46~2 0.22 1 PI Rat peroxisomal acetyl-CoA ac}4tTanslarase 4701 0.04 Bovma endozepine related protein 4704 0.04 2q31-q32 , Human ~n 4712 0.04 Mouse secreted isoform neural cell adhesion mdecule (N-CAM 120) 4719 0.04 Human MAP kinase activated Protein kinase-2 4722 0.04 Rabbit titin 4?49 0.04 Xp11.3-p11.23 Human properdn 4767 0.04 3q22-q25 Human pdyadenylate binding protein 4773 0.04 Chicken smooth muscle myosin light chain kinase, 4774 0.04 Helianlu= e. pollen specific protein SF3 4804 0.13 Rat mitochondrlal cerni~ne pal,m,!toyItrenlfersee 1 48O6 0.01 Xq2S.1 Human h)1>oxan~ine phcephoribos~trm sferase ,. 4~2~ 0.01 1 BR ,,,, Yeast generd ne,qative regulato~ of trane•iption subunit 1 (NOTI) 4843 0.01 BR 9 Human J kappa +ecombinaison ,,;~nal bindin~ protein pseudogene 1 4939 0.01 Mouse protein-I~osine phosphatase kappa 6857 0.01 I(~p13.'I IHumen GSTI-ItS GTP-I~ndm 9 prmain 4962 0.01 3 eR 17o~4.qtw Human nuclear p68 protein 4986 0.01 Yeast Klualene monooxyejenace 49O3 0.01 IMouse necdin S003 0,01 'E. ¢oli i acetolactate ,,ynthase hsozyma IIIr I chain 5O17 0,01 1 HL Yeast , protein SLYI 9826 0.01 ,Human ! putative ribosomal protein L13 S062 0,01 Human +metebotropic 9lutomate te~pW 5+ 5o64 0.02 I 'BR Yeast poasible 1.ac~-en-gtycerd-3.phoaphate acyltra~sferase 5O85 0.01 Human glyclne cleavage system H Protein 5133 0.01 C. elegane hypothe6cd 58.3kd Protein F42H10.7 in chromosome ill 5134 0.0! Mouse zinc-finger Protein Bfimp-1 516g 0.01 1 CC E. ¢oli isoleucybtRNA a),nthetase 5172 0.0i ~ompmtia ring canal Protein KELCH 5179 0,01 3 BR Human CDC4 related protein ,, 5263 0.01 Drosophille REF (2tP protein 5293 0.01 2 F~ Rat pho~ohaSdylinolitd tranabr protein 5311 0.01 Human GP36b ,¢jlycoprotein 5336 0.01 ,, Hum,an randomly sampled cDNA D13763 5343 0,01 Vaocinia virus protein C3 Precursor 5351 0.01 ,,,, Mouse )uta~e EC*8 ~40g o.ql ,, , Human PINCH (a ne~v,LI M protein) 5436 0.02 2 BR Bovine cellular retinaldehyde-bind~ng protein 5447 0.01 1 BR Human ribosomal protein 1.23 ~474 0.01 Mouse cytotoxic T-cdl membrane ,91yooprotein Ly-3

302 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

GENEXPRESS INDEX

Appendix 1C: Related gene transcripts (continued)

0.01 Mouse brain protein DN38 . 6soo ,OOl, ~ H~,P~ , 6 Yeast P24B protein 6~o7...... 0.01 , 2O ,, Rat 66,1q.... 001 , 16 ...... I~13.3 Humarl l>dyoy~ kidney disease 1 Protein 6660 0.01 ~t golgi appara~ua aialoglycoprot~n MG-160 ss~6 o.oi ' 17 .... Mouse, brain protein H5 ,, 0.01 :~ Yeast, NIF~.like 54.5kd Protein. . . 66t0 0.01 16 Human DNAJ Protein homdi=j O.Ol 4~7 Human brain ankyrin ms i 0.o1 6 .~,~R,cc ...... J Bombyx mori"' ,, ,, atanyl.tnNA ~/n~tetase .... 6~oe 0.01 ...... Mouse zine-fin,q,er Protein ZFP-27 S714 0.01 Human hnRNP-F~. ,,, 6717 0.01 , ,, ,,,,,,, Mouse Rab-t 8 S722 0.01 C. ~egens 5~Z'~ ...... 0.01 ,, E. ¢oli aminopeptidsse A/I ...... 5724 0.01 ~ BR,FB 17 Hurna,,n .... gamma tubulln ....sBil o.oi ...... 3p21,-p22 Human ~nc 6nger protein ~116 , , 0.01 ..... 17 Ye~t h~x~he~c,~ 34.9 kd protein in LIRA! $831 0.01 1 9q34.1 Humqn, eden)4ate kinase i~oenzyme 1 ,, ,~ o.oi , iq~.I Human,, MAP kinase phoephatase I $647 0.01. I BR Yeast ubiquitin oarboxy~.terminsl 4 ~sO 0.01 3 BR se¢61 horn do~ue ...... , O.Ol, 19 11~3 IHuman zinc Eng~ ~otein HR X 5876 0.01 I rc~osm4ium myoein light dlein kinase 68B2 0.01 1 BR Yeast I NAM7 protein {probable heiioase) , 0.~ 2 iAmphoxius ! cAyp-tar~e, ~,ote, ...... 6078 0.04 6 ~b~t P.59 X Xp11.4-p11 3' Human mono~mine oxidase 9 6001 0.04 12 !Yeast, ~'ensoriptior~t acIvator GCN3 6o~5 0.04.... ,,,, 19 Human Kruppel.type zinc fil~.,ger 6123 0.01 X IC. elegans h~o~a~oai z~6u protein ~42H101~in g;kmo;,o~ ,, 6156 0.04 3 4p16.3 IHuman ~osmid clone HDAB ~1S149 I L • .....6!r~. 0.04 I0 Xenopus , ubiqultin4ike fueion promin L, 6192 0.04 1p31 Human, ,, ! glucose transporter t~pe 5, 6190 0.04 Rat pro~u~ ...... 6209. 0~04 . . Wheat ubiquitin.conjuga~n9 enzyme E2-20.kO , 6237 0.04 1 pl Human, ' ribosomal Protein 1.4 ...... 6240 0.04 Human liver 6.phosphof~u,ct,skin asa 6282 0.04 ,,, Rat mitochondr!al osrr~tine palmitoyIVansferase 1 ~, 6~89 0.04 17p!~-p12 Human p~inatal cardiac m~osin h .eavy chain 6=s 0.04 mm peptide chain release factor 2 .,o 004 n~m Human =mCluen(~, M770~4 !,s,olatedI~ cross:reaotivib/, of ARF sera 6371 0.04 Yeast, ABCI protein ...... 6374 0.04 Human ubiquitin ...... ,6~,~ .... o~04 .. IE[] Rat ~rohibifin 63B 3 0.04 9q22 Human ~'opomodui'i'n 6391 0.04 2q31 -q32 Human titin 0.04 = II~ Drosophilia ubiquitin-con,jugatin 9 en~ .m.e E2-16 kO ..... 6414 0:04 II~m Drosophifia . BRAHMA protein 6417 0.04 17pter-p11 Human -1 embryonicllfa,st skete.ta! muscle myosin hea~ chain , ~e ...... 0.04 i E. ooli DNAJ protein ~Hl,, o~ , 17 17ptar-p12 Human :Derinatalcardiac myosin h .e,a,,,vy chpin 646~ 0.04 E. co, glutam~4-tRNA synthetasa 6472 0.04 Human UDP.91ucose pyrophosphor~ase, 6478 0.04 20 Yeast hypothe~oai 44.1 kDa protain .... . e,m 0.02 Vaccinia virus , protein .K4 .. 6486 0.04 , i 1 Yeast ABCI protein 6511 0.04 I ...... 3 ..... Mouse cytoplasmic 91ycerol-3~phosphate dehydro.qenase 6~3 o.04 , ,,,,, 9q~ ...... Rabbit ! .sercolumenin . . 664,s, 0.04 / 3 Human tropomodulin 6550 0.04 Human =pregnancy-specific beta.1-91yeoprotein-11 6as ! 0.04 Bovine mit.ochondrial eden,/late kinase 3 6557 0.04 ...... , ...... i..... 12 !, Hamster : mevalonate tTansporter . . 6558 0.04 Human i peptidylproline cis.Fqns isomarase ..... 65"/3 0.09 0.01 ! .... Sr 8 Mouse .... i muscle-brain cAMP dependent protein kinase inhibitor (PKl.alpha) ' 6577 0.04 14+16 Human pdyadenylate binding protein 65B3 0,04 .. 2 Chicken I tltin ...... 6586, I 0.04, Xallop~,$ ,,, t, enac,ip~o, factor 3A ..6~I I o.o4 17 Human l ~ ,ort'~ain specili? acff-CoA ,de,~,droger~se 6== 0.04 .... i ..... 22q13;31:qter-, Human NADH-cytochrome B5 reductase 6610 0.04 mm 9 Dictyostdium vegetative specili¢ protein H7 66~o 0.04 mm Schistosoma ,m. hemocjIobinase .s~3. 0.04 ..... 22 12 Human tubu,n =ph a 4 6648 0.04 E. cdl insertion element 5 66~ o.oi ...... C. elagans hyp~a6~-' ~.0kd protein zK~2.12 in ohro~o,o~a ,,, 6766 0.01 Human ADP-ziboa~ation factor 1 6739 0.01 Huma.nj ¢oatomar ,beta' subunit 6743 0.01 I:ll]lll~l Iong*chein-lattpacid-CoA ligase 6760" 0.01 " ~rot~,-, kinasa 2 6771 0,01 Bovine vacuolar H+ATPase wJbu~t A 6776 0.01...... Human HS,p binding immunophilin P59 6771) 0.01 C. eiegans h~potheEcai 64.5 kda protein ZK652.9 6792 0.01 Maize homeolic protein knotted.1 680~ ...... 0.01 21q22.3 Human cyatathionine bete.,sp~ase 6814 0.0t Rat calmodulin-depenobnt proWin kinase 2 delta ..~. 0.oi 1 HA C. elecjons putative ATP,depandent RNA helicase T26G 10.1 in chromosome til r~38 0.01 19¢l.13.2,q13.4 Human zinc lincjer protein ZNF42 61149 0.01 brain alpha-tropomyoein TMBr-3 I Rat o.oi 11q23.1-q23. 2 Human, zinc fir~, er ZNF128 687O .... 0.01 Yeast d~ta.1-py~oEne.5-cerbox~ate ~,y~ogenas e 6871 0.01 4q12<121 Human krueppel related DNA bindin~ protein (PF4) 6a76 O.Ol I HA Rat CaBP1 calcium binding, protein

GENOME RESEARCH @ 303 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

HOULGATTE ET AL.

Appendix 1 D: Unknown gene transcripts (partial) ~,,~, , S~ I l"l**u,, :' am r',mmm~ LLHI,L I mm 2:)00 4627 o.o,, i r,m,mn m ~o nnmmm 4628 o.o4 i t9 2212 rT:rmmnml~ .4629 3213~'4 m';xrImmm i~ 46so ] m mmm,;1';'Iimdm*-,* a: mmm mammm .4631 0.o4 , ,3,,, • mmmmmmm~m m:n S21S m~mnm .4632 O.O4 8 ,'~mmmn--,:~: i [~'~lmUl~ ...~4633 0.~ ' 1 ,~~~ m ll~imu~ 0.04 ...... 1 ~iB I am :me mamn 4~S o:~ !.... s--- ]i~ II III I~ ~mnm 0,04 I 6 I HI'FB,BR 14 ~iOam[:mmmmmm o-°~ I I 3 0.o= I t I~' ,8

Appendix 1 E: New gene transcripts in known regions

~own U~k~ Unknown

Unknown

Unknown Unknown ~k~o~

Appendix 1 F: Overlapping gene transcri ~)ts

Overt U~ des oN pr~l.et ~ DNA-dkected RNA erme II 33kd "de Unknown .~ENX.S139 -- Unkamm

i "d ~m I~d(~l l.lum~ P Unl~m ne r lot on sul~t - acid tra t olein Ur~ewn _h." !RNA ~, Ur~o~ T~ ~m e mined I hem ~ nm~,nhal a~Jm~ ~ ~'ot~n d -7 1

,

Appendix 2A: eSTS markers (partial) '#~I~qiL~]nLqK[quL~L CCAACAGGCTCTTGGATGAC I 128l 1300 l 4 IDTS2134E ~[~!~¢[~(,~.,Eqf331~ CTTACGCATTCTTGGCACAC l, ~1 ~o5 7 [DXS7O~ ~/~Jf.~f~.v~L~f:~.T~ ~GTITrCCTTTGGCGTATGAC I 101] 101 , o ID~S~MOE .:~ ~-. ,, -~ : ,I"rTaTAGCACCOSTCTqTCC ! 1101 11(~ ImCSS~e CCCGAC~TTTOCAAATGTTC ATCTCT'rACATCTCTCACCC I ~071 i071 . ioxs~,s ~.,CAAACCCCAAGTCCTCAC AA/~=GTCTTCCCAGAGACAC I 1591 IS9J C~.OTCOT*Cl"OOC~O~ acvuv~cc~Gac, Gaaatt~c I ~,~1 196] ,14 lo~sHsTs GCTTrGGTTGTTTGCTTTCTGG ~T'GAAGATGGATGGGATTGTG I 16811~88 is i~2S~E CCCTGCCCTCACTCTAAG ~,CTGCTGATACATGCAACAACC I 18 I01~1246E CCTGTTGATGGAGTGGTGTG 3CTGCTGATGCTGAGAAAGTG I "~1 "fl '"10 io~2s~2oss ! GGAAGAGACAATCACAACTCAC ~CTCTGCTCTGATCTrTTAGG | 105| 105J ,= lo~,,=s '1 AACl"rGGAATTACTGGGTGGG ~,,TAGGATGGGGACTGGG I 174| ~74I iO~TS~~°se, I AC-~-.CT(~ATCAO~,C rCCCA'rTTGTTTCrCACACCC I ~a41 ~41

Appendix 2B: Accession number)er cross-index cross-i (partial)

I = I r~9 I r-oos,s I r.oo~s Fooogo r~is7 t ,=,7 I z,,~5 Z45589 #1"03897 i , R | #Zl7415 I #Z21830 I #Z21832 k_t'~ ! z41zle Z45590 s I Fo~ I r~'~s I ~' ~7os r~ 23O9 Z41280 Z45591 $ | F06696 I F06716 I F08458 #M62187 #Z17832 2"~o z412sl F08269 4 I F01528 I Z39764 [ F05275 Z43704 "'~3~I z4ss~ i = I z=~2 I. z43~o I '=== Fo,~7 F02587 F02676 ! ' Z40181 Z41950 e I z3~ I Fo6~7 I. i~'2312 F06297 Z43223 Z44209 ] #T03617 I #T17387 7 I Z3o.~s I z,3~ I. l 2a~s ! FO4SOo F08271 . ..e IZ3~I Z43~1 2314 ] Z41284 Z45596 I ' g / Z39.~o I Z43~s I ~r~o>4o '" 2316 Z39060 "FO4SO3 Z4s~7 ~rossgo I 10 I, F02728 1 F0S443 I#D208421 z45sge ...

304 ~ GENOME RESEARCH Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press

The Genexpress Index: a resource for gene discovery and the genic map of the human genome.

R Houlgatte, R Mariage-Samson, S Duprat, et al.

Genome Res. 1995 5: 272-304 Access the most recent version at doi:10.1101/gr.5.3.272

References This article cites 87 articles, 10 of which can be accessed free at: http://genome.cshlp.org/content/5/3/272.full.html#ref-list-1

License

Email Alerting Receive free email alerts when new articles cite this article - sign up in the box at the Service top right corner of the article or click here.

To subscribe to Genome Research go to: https://genome.cshlp.org/subscriptions

Copyright © Cold Spring Harbor Laboratory Press