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0.01 Sequence Description Accession #Fold Change P-Value Solute Carrier Fa

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FD WT untreated with DMH versus FA WT untreated p <0.01 Sequence Description Accession #Fold Change P-value Solute carrier family 9 (sodium/hydrogen exchanger),NM_016981 member -1.180931 0.00071 RIKEN cDNA 4933433P14 gene NM_178613 1.18204 0.00021 BTB (POZ) domain containing 15 NM_172765 -1.18226 0.00048 CDNA sequence BC012278 NM_146231 1.18552 0.00035 CDNA sequence BC052040 NM_207264 1.18811 0.00073 Unknown -1.18918 0.00083 Transmembrane protein 45b NM_144936 -1.19374 0.001 Zinc finger, matrin type 5 NM_026015 -1.19969 0.00027 T-complex 11 (mouse) like 2 NM_146008 -1.19983 0.00034 Villin-like U72681 -1.20146 0.00074 Zinc finger protein, multitype 1 NM_009569 1.20364 0.00028 PREDICTED: similar to ring finger and KH domainAK037256 containing 2 -1.20617 [Mus musculus], 0.00029 mRNA sequence Kinesin family member C2 NM_010630 1.20891 0.00038 RIKEN cDNA 2810407C02 gene BM945607 -1.21247 0.00022 Ganglioside-induced differentiation-associated-proteinNM_010269 2 -1.21278 0.00034 Integrator complex subunit 5 NM_176843 -1.2137 0.00037 Lectin, galactose binding, soluble 8 NM_018886 -1.21525 0.00085 WSB-2 protein NM_021539 -1.21853 0.00011 Expressed sequence C80913 NM_011274 -1.22306 0.0002 Expressed sequence AW061290 NM_201361 -1.2266 5.22E-06 Mus musculus 2 days pregnant adult female ovaryAK054427 cDNA, RIKEN 1.22687 full-length 0.00038 enriched library, clone:E330024N10 product:unclassifiable, full insert sequence. CEA-related cell adhesion molecule 1 BC042780 -1.22753 0.0009 Aryl-hydrocarbon receptor-interacting protein NM_016666 -1.22758 0.00004 Chloride channel calcium activated 6 NM_207208 1.22912 0.00051 SAPS domain family, member 3 NM_029456 -1.22952 0.00042 ATPase, Na+/K+ transporting, beta 1 polypeptideNM_009721 -1.22954 0.00004 Mus musculus zinc finger protein 120 (Zfp120),NM_181267 transcript variant1.2304 3, mRNA. 0.00027 Ataxia telangiectasia and Rad3 related AF236887 1.23079 0.00001 Centrosomal protein 70 NM_023873 1.23115 0.00079 Solute carrier family 35, member D2 AK017526 -1.23159 0.00001 Zinc finger protein 287 AK029572 1.23405 9.63E-06 Uridine-cytidine kinase 1 NM_011675 -1.23409 0.00039 RIKEN cDNA 2310050N03 gene AK009502 1.23485 0.00033 Mus musculus 16 days embryo head cDNA, RIKENAK048085 full-length -1.23503enriched library, 0.00077 clone:C130033N23 product:unclassifiable, full insert sequence. KIAA0251 hypothetical protein AK048881 1.23622 5.57E-06 H1 histone family, member 0 NM_008197 1.24222 0.00016 Protein phosphatase 1, regulatory subunit 10 AK004266 1.24294 0.0003 Metal response element binding transcription factorNM_008636 1 -1.24401 0.00037 Mus musculus DNA segment, Chr 10, UniversityNM_178606 of California at-1.24488 Los Angeles 0.00019 1 (D10Ucla1), mRNA. Acid phosphatase-like 2 NM_153420 1.24791 0.00003 Damage specific DNA binding protein 2 NM_028119 1.24812 0.00006 RIKEN cDNA 1110021L09 gene AK003902 1.24929 1.11E-06 DNA methyltransferase (cytosine-5) 1 NM_010066 1.25058 0.00003 Ankyrin repeat domain 49 NM_019683 1.25147 0.0002 Cytochrome P450, family 39, subfamily a, polypeptideNM_018887 1 1.25215 0.00007 BC022110 aminolevulinic acid synthase 1 {Mus musculus}, partial-1.25225 (5%) [TC1048789] 0.00018 Rho GTPase activating protein 20 NM_175535 -1.25331 0.00003 Replication factor C (activator 1) 5 AK011489 1.25355 0.0001 Transmembrane protein 106B NM_027992 -1.2536 0.00065 Ataxia telangiectasia and Rad3 related AF236887 1.25374 4.25E-06 RIKEN cDNA 5730596K20 gene NM_146091 -1.25505 0.00029 Caspase recruitment domain family, member 6AK052796 1.25536 0.00001 Serine/threonine kinase 39, STE20/SPS1 homologNM_016866 (yeast) 1.2569 0.00066 ATXX_MOUSE Ataxin-10 (Spinocerebellar ataxia type 10 protein1.25854 homolog) 0.00064 (Brain protein E46). [Mouse] {Mus musculus}, partial (27%) [TC1029420] MOB1, Mps One Binder kinase activator-like 1AAK077320 (yeast) -1.26148 0.00073 NCK-associated protein 1, mRNA (cDNA cloneAK083469 IMAGE:3488144) 1.26169 1.82E-06 Ribonucleotide reductase M1 NM_009103 1.26253 0.00013 Eph receptor A4 NM_007936 1.2627 0.00003 Coiled-coil domain containing 28A NM_144820 -1.26342 0.00052 Cytochrome P450, family 27, subfamily a, polypeptideNM_024264 1 -1.26594 0.00041 Kv channel interacting protein 4 AK017706 1.26809 0.00091 Tripartite motif-containing 36 NM_178872 -1.26869 0.00009 Pyroglutamyl-peptidase I NM_023217 -1.2698 0.00025 Matrix metallopeptidase 19 NM_178066 1.26989 7.95E-06 Signal-induced proliferation-associated 1 like 1AK043743 1.2705 0.00008 Cytochrome P450, family 4, subfamily a, polypeptideX71478 10 -1.27128 0.0007 Bystin-like, mRNA (cDNA clone MGC:27710 IMAGE:4925307)NM_016859 -1.27161 0.00009 Stathmin 1 NM_019641 1.27316 0.00001 Retinol dehydrogenase 10 (all-trans) NM_133832 -1.27503 0.00026 Expressed sequence C80913 NM_011274 -1.27785 0.00002 Membrane-associated ring finger (C3HC4) 9 BC019560 -1.27794 0.00013 Sorting nexin 11 NM_028965 -1.27953 0.00006 Activating transcription factor 2 NM_009715 -1.2812 0.00004 RB-associated KRAB repressor, mRNA (cDNA NM_021326clone MGC:699061.28225 IMAGE:6825552) 0.00049 Sideroflexin 5 NM_178639 1.28477 2.17E-07 RIKEN cDNA 9030612M13 gene NM_172458 -1.28581 0.00016 Nemo like kinase NM_008702 1.28593 0.00094 Bromodomain and WD repeat domain containingAK083676 3 -1.28713 0.00084 Mdm2, transformed 3T3 cell double minute p53NM_134092 binding protein1.28804 2.05E-06 RIKEN cDNA 1500034J01 gene BC034701 -1.28869 0.0004 Ubiquitin specific peptidase 37 AK077383 1.2896 0.00032 NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)NM_026277 -1.28964 0.00079 Microtubule-associated protein, RP/EB family, memberNM_153058 2 -1.28978 0.00042 Ankyrin repeat and SOCS box-containing proteinNM_023906 3 -1.29059 1.51E-06 RAB22A, member RAS oncogene family NM_024436 -1.29297 0.00062 RIKEN cDNA D230010M03 gene AK080671 1.29559 0.00007 F-box only protein 32 NM_026346 1.29584 0.0003 Mus musculus splicing factor, arginine/serine-richNM_177199 10 (transformer1.29873 2 homolog, 0.00001 Drosophila) (Sfrs10), mRNA. Tropomyosin 3, gamma NM_022314 -1.30011 7.83E-06 Protein arginine N-methyltransferase 6 AK034732 -1.30045 0.00007 expressed sequence AI504630 AK004302 1.30128 6.64E-07 Nuclear factor I/C NM_026756 1.30258 5.30E-06 Proviral integration site 3 NM_145478 -1.30274 4.09E-07 Ring finger protein 41 AK044103 -1.30333 9.91E-06 Replication factor C (activator 1) 4 NM_145480 1.30395 5.58E-07 ABI gene family, member 3 NM_025659 -1.3049 0.00042 Nuclear receptor coactivator 4 AK014479 -1.30565 0.00025 Coiled-coil domain containing 25 NM_145944 1.30644 0.0002 RIKEN cDNA 4833409A17 gene BB781167 1.3067 0.00002 PAS domain containing serine/threonine kinaseNM_080850 1.30679 3.66E-07 Deiodinase, iodothyronine, type I NM_007860 -1.30809 1.13E-07 Unknown 1.30832 0.0002 Phosphoribosyl pyrophosphate synthetase-associatedAK082484 protein -1.310451 0.00078 10 days neonate skin cDNA, RIKEN full-length AK084197enriched library, 1.31061 clone:4732460I02 0.00003 product:unclassifiable, full insert sequence Unknown -1.31142 0.00039 RIKEN cDNA 0610007N19 gene AK002304 1.31212 0.00016 Plasma membrane proteolipid NM_026385 -1.31238 0.00004 Mitogen activated protein kinase kinase kinase AK0291312 -1.31456 8.89E-06 Plexin B1 NM_172775 1.31477 0.00048 Angel homolog 1 (Drosophila) NM_144524 -1.31556 0.00093 pericentrin U05823 1.31613 0.00082 RIKEN cDNA 1300010M03 gene NM_026501 -1.31649 0.00049 Sno, strawberry notch homolog 1 (Drosophila) BC027253 -1.31864 0.0006 Casein kinase 1, delta NM_139059 -1.31906 0.00033 Mus musculus RIKEN cDNA 1110006O17 geneXM_148854 (1110006O17Rik),1.3202 mRNA 0.00044[XM_148854] RIKEN cDNA 2310047C04 gene AK122344 1.32097 0.00033 RIKEN cDNA 6030413G23 gene AK045461 1.32155 0.00001 RIKEN cDNA 2210020M01 gene NM_183259 -1.32231 1.85E-06 Phosphodiesterase 1B, Ca2+-calmodulin dependentNM_008800 1.32252 0.00023 Fer-1-like 4 (C. elegans) AK018656 1.32382 0.0009 Tumor necrosis factor receptor superfamily, memberNM_009400 18 1.32687 0.00001 Deoxyribonuclease I, mRNA (cDNA clone MGC:40629AA041580 IMAGE:4913032) 1.32722 0.0001 Degenerative spermatocyte homolog 1 (Drosophila)NM_007853 -1.32907 0.00001 Nuclear factor of kappa light chain gene enhancerNM_010907 in B-cells inhibitor,1.32916 alpha 0.00083 ADP-ribosylation factor-like 13B AK016794 -1.32935 8.45E-06 Mus musculus TSPY-like 4 (Tspyl4), mRNA. NM_133745 1.32989 0.00068 RIKEN cDNA 4933431E20 gene NM_177858 1.33086 0.00045 Excision repair cross-complementing rodent repairNM_146235 deficiency complementation1.33443 0.00097 group 6 - like Rho GTPase-activating protein NM_177379 -1.3351 0.00062 High mobility group box 1 BC064790 1.33558 0.0009 Interleukin 7 NM_008371 -1.33716 0.00003 Mitogen activated protein kinase kinase kinase NM_0077468 1.3377 6.26E-06 BCL2/adenovirus E1B interacting protein 1, NIP3NM_009760 -1.33867 0.00005 DNA segment, Chr 4, Brigham & Women's GeneticsAK008061 0951 expressed 1.33946 0.00067 CCR4-NOT transcription complex, subunit 6-likeNM_144910 -1.33958 0.00086 CDNA sequence BC056923 NM_173395 1.34106 0.00034 Syntaxin 5A NM_019829 -1.34127 1.96E-06 Unknown -1.34276 0.00001 Unknown 1.3439 0.00008 RIKEN cDNA 2610507N02 gene AK012069 -1.34485 0.00061 CDC14 cell division cycle 14 homolog B (S. cerevisiae)NM_172587 -1.34504 0.00032 Activator of basal transcription NM_013924 -1.3468 0.00009 RB-associated KRAB repressor, mRNA (cDNA NM_021326clone MGC:69906-1.34713 IMAGE:6825552) 0.00025 Polymerase (DNA directed), epsilon NM_011132 1.34746 4.26E-07 DNA segment, Chr 14, ERATO Doi 581, expressedAK045133 1.34755 0.00034 RAD52 homolog (S. cerevisiae) NM_011236 1.34761 0.00083 RIKEN cDNA 2810458H16 gene AK013364
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  • Supplement 1A Steffensen Et

    Supplement 1A Steffensen Et

    Liver Wild-type Knockout C T C T 1 2 4 7 8 9 1 2 4 5 7 9 1 1 1 1 1 1 C C C T T T C C C T T T W W W W W W K K K K K K IMAGE:793166 RIKEN cDNA 6720463E02 gene IMAGE:1447421 ESTs, Weakly similar to ZF37 MOUSE ZINC FINGER PROTEIN 37 [M.musculus] IMAGE:934291 RIKEN cDNA 2810418N01 gene IMAGE:1247525 small EDRK-rich f2actor IMAGE:1449402 expressed sequence AW321064 IMAGE:1279847 ESTs IMAGE:518737 expressed sequence AW049941 IMAGE:860231 a disintegrin and metalloproteinase domain 17 IMAGE:642836 CD86 antigen IMAGE:1003885 phosphoribosyl pyrophosphate sy1nthetase IMAGE:524862 RIKEN cDNA 5730469D23 gene IMAGE:1264473 protein inhibitor of activat1ed STAT IMAGE:847035 RIKEN cDNA 4833422F06 gene IMAGE:374550 requiem IMAGE:976520 nuclear receptor coact4ivator IMAGE:1264311 Unknown IMAGE:976735 expressed sequence AI987692 IMAGE:976659 cathepsLin IMAGE:1477580 RIKEN cDNA 1600010J02 gene IMAGE:1277168 ribosomal protein, large, P1 IMAGE:524842 RIKEN cDNA 0710008D09 gene IMAGE:373019 split hand/foot delete1d gene IMAGE:404428 expressed sequence AI413851 IMAGE:619810 RIKEN cDNA 1700003F10 gene IMAGE:1749558 caspase 3, apoptosis related cysteine protease IMAGE:718718 RIKEN cDNA 2810003F23 gene IMAGE:819789 Unknown IMAGE:524474 ATP-binding cassette, sub-family A ABC1, member IMAGE:804950 Mus musculus, Similar to ribosomal protein S20, clone MGC:6876 IMAGE:2651405, mRNA, complete cds IMAGE:806143 gap junction membrane channel prot2ein beta IMAGE:1745887 expressed sequence AI836376 IMAGE:779426 RIKEN cDNA 5230400G24 gene IMAGE:1125615 Unknown IMAGE:535025 DNA
  • Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant

    Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant

    Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7,
  • (19) United States (12) Patent Application Publication (10) Pub

    (19) United States (12) Patent Application Publication (10) Pub

    US 20120149714A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0149714 A1 Heise et al. (43) Pub. Date: Jun. 14, 2012 (54) EFFECTS OF INHIBITORS OF FGFR3 ON (60) Provisional application No. 60/748,944, ?led on Dec. GENE TRANSCRIPTION 8, 2005. (76) Inventors: Carla Heise, Benicia, CA (US); Publication Classi?cation Esther Masih-Khan, Ontario (CA); 51 I Cl Edward Moler Walnut Creek CA ( ) nt' ' (US); Michael. Rowe,’ Oakland,’ CA A61K 31/497 (2006.01) (US),_ Keith. Stewart, Scottsdale, G01N 33/53 (2006.01) AZ (US) Suzanne Trudel Ontario G01N 33/566 (200601) (CA) ’ ’ C12Q 1/68 (2006.01) (52) US. Cl. ................ .. 514/253.07; 435/611; 435/612; (21) Appl. No.: 13/400,833 435/79; 435/792; 436/501 (22) Filed: Feb. 21, 2012 (57) ABSTRACT Related U‘s‘ Application Data Methods of utilizing blomarkers to 1dent1fy patients for treat ment or to momtor response to treatment are taught herein. (62) Division of application No, 12/096,222, ?led on Jun, Alterations in levels of gene expression of the biomarkers, 19, 2008, now Pat. No. 8,158,360, ?led as application particularly in response to FGFR3 inhibition, are measured No. PCT/US2006/061766 on Dec. 7, 2006. and identi?cations or adjustments may be made accordingly. US 2012/0149714 A1 Jun. 14, 2012 EFFECTS OF INHIBITORS OF FGFR3 ON [0007] An individual’s response to a particular treatment or GENE TRANSCRIPTION predisposition to disease and the correlation to a particular gene of interest has been documented. It is noW believed that BACKGROUND OF THE INVENTION cancer chemotherapy is limited by the predisposition of spe ci?c populations to drug toxicity or poor drug response.