Gene Expression Report

Isogenic Cell Lines Common Genes

CAGED Report (November 17, 2009) Isogenic Cell Lines Common Genes

Materials

The complete database comprises 16 expression measurements of 1242 genes. The recorded expression values range between -3.66003 and 3.839347, with an average expression value of -.000.

Methods

The analytical task is to partition the genes into clusters sharing a similar behavior over the 16 different conditions. This cluster analysis was performed using CAGED (1).

A Bayesian approach assumes that the observed data were generated by a set of unknown processes. We do not know how many processes are responsible for the observed data, and the clustering process aims at identifying these processes. We define two gene profiles as similar if they were generated by the same process. In a Bayesian framework, we can define this similarity measure as the posterior probability of a clustering model - i.e. a way of grouping individuals into groups - given the observed data. The clustering method adopted herein starts by assuming that all clustering models are equally probable (i.e. assuming a uniform prior distribution over these models), computes the posterior probability of each model given the data, and selects the most probable one. This approach spares us the effort of defining an arbitrary similarity threshold to decide whether two individuals are similar and has the further advantage of taking simultaneously all the data into account, rather than looking at single pairwise measures of similarity.

We assume the observations to be generated by a polynomial model of order 6, and set the prior precision and the gamma value to 1 and 0, respectively. Polynomial models capture the pattern of dynamics along time. The prior precision is the size of the sample upon which the prior distribution is built, while the gamma value is the rate to zero of the prior precision, with 0 representing the case of perfect ignorance. The method requires a similarity measure to guide the search procedure and a Euclidean distance distance measure between gene profiles was adopted. Note that this measure is used only for search purposes and it is not involved in the actual decision to merge a set of gene profiles together. Goodness of fit of the resulting model is assessed by checking the normality of the standardized residuals of each cluster. Details about this clustering method can be found in (1).

Results

The cluster analysis described in the Methods section yields 33 clusters. Figure 1 draws the expression profiles of the members of each cluster.

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Figure 1. Plots of individual gene expression profiles partitioned by cluster membership. Click on the images to enlarge.

Figure 2 shows the dendrogram of the hierarchical structure of the clustering model together with the gene expression profiles (2). The left hand side of the picture shows 33 parallel hierarchies, one for each identified cluster. The order of the clusters follows, from top to bottom, the indexing reported in Table 1. Integers at the branching points of the trees report, on a logarithmic scale, the Bayes factor of each merging. The Bayes factor is the ratio between the posterior probabilities of two models and, in this case, indicates how many times more probable is the clustering model in which the two branches are merged than the clustering model in which they are kept separated. The central part of the drawing displays the expression values of each gene expression profile. Expression values higher or lower than 0 are reported in two different colors. The intensity of each color is proportional to the distance of each value from the cutpoint 0. The last row reports a brief description of each gene in the database.

Figure 2. Display of the hierarchical structure of the clustering model. The left hand side of the picture shows the tree structure of each discovered cluster. Numbers at the branching points of the trees report, on a logarithmic scale, the Bayes factor of each merging. The Bayes factor is the ratio between the posterior probabilities of two models and, in this case, it indicates how many times more probable is the clustering model in which the two branches are merged than the clustering model in which they are kept separated. The central part of the drawing displays the expression values of each gene expression profile. Expression values higher or lower than 0 are reported in two different colors. The intensity of each color is proportional to the distance of each value from the cutpoint. The last row reports a brief description of each gene in the database. click here to see an enlarged version.

file:///C|/...ferential analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED.html[11/17/2009 1:43:24 PM] Isogenic Cell Lines Common Genes

Figure 3 draws the expression profiles of each of the 33 identified clusters. A cluster profile is the prototypical behavior of its members computed as pointwise average of the gene profiles comprises in the cluster.

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Figure 3. Plots of the profiles of each discovered cluster. Each profile may be regarded as the prototypical behavior of its members across the different conditions and it is computed as pointwise average of its cluster members. Click on the images to enlarge.

The basic terms of the statistical model of each cluster is reported in the part of Table 1. Each cluster is indexed by a number. The second column shows the number of individual gene expression profiles in each cluster. The third and fourth column report the basic terms of the statistical model of each cluster: residual sum a squares and linear regression coefficients.

Residuals Index Elements RSS Coefficients Mean SD Skewness Kurtosis .804 -1.188 .624 -.144 1 25 61.110 -1.896 1.535 .406 2.948 .016 -.001 .000 -.255 .199 -.110 .019 2 23 16.622 .377 1.024 .126 4.981 -.001 .000 -.000 -.067 .550 -.247 .045 3 38 39.915 .093 1.092 -.100 2.772 -.005 .000 -.000 -.857 1.397 -.681 .140 4 40 29.337 3.811 1.151 .346 3.808 -.015 .001 -.000 -.255 .502 -.262 .056 5 37 16.648 .769 1.052 -.040 2.902 -.006 .000 -.000 -.219 .042 -.066 .024 6 140 60.172 .147 .950 -.105 2.936 -.003 .000 -.000 -.527 .113 -.111 .039 7 68 46.538 .938 1.031 -.045 3.596 -.005 .000 -.000 -.748 .832 -.439 .098 8 26 25.021 2.222 .758 .252 4.033 -.011 .001 -.000 .068 -.452 .228 -.047 9 37 23.814 .133 1.731 -.012 2.216 .005 -.000 .000 .192 -.931 .397 -.064 10 43 37.055 .035 3.140 -.575 2.185 .005 -.000 .000 .317 .164 -.032 -.006 11 56 33.600 -.120 1.014 -.036 3.183 .002 -.000 .000

file:///C|/...ferential analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED.html[11/17/2009 1:43:24 PM] Isogenic Cell Lines Common Genes

.191 -.049 .053 -.017 12 70 30.807 -.162 .951 .267 3.091 .002 -.000 .000 .527 -.845 .427 -.087 13 73 59.951 -.913 1.644 .166 3.287 .009 -.000 .000 -.212 1.090 -.469 .083 14 117 89.940 1.366 1.198 .198 4.329 -.007 .000 -.000 -.446 .686 -.315 .054 15 72 52.607 1.331 1.065 .572 4.166 -.005 .000 -.000 -.701 .349 -.193 .042 16 43 27.017 2.015 1.283 .330 2.957 -.004 .000 -.000 .109 -.213 .128 -.027 17 52 34.851 .932 1.312 .041 3.209 .003 -.000 .000 .130 .237 -.047 -.002 18 46 66.127 .742 .728 .536 4.107 .002 -.000 .000 -.740 .747 -.319 .049 19 19 20.300 1.800 1.021 .747 5.029 -.004 .000 -.000 -.241 -.780 .315 -.046 20 46 57.773 -.300 2.679 -.286 2.127 .003 -.000 .000 -.712 -.350 .057 .018 21 28 38.171 .060 2.147 .111 2.350 -.005 .000 -.000 1.276 -1.027 .494 - 22 16 25.750 -1.504 2.179 -.832 3.373 .097 .009 -.000 .000 -.272 -.201 .072 -.010 23 18 28.534 1.265 1.995 .189 2.025 .001 -.000 .000 .348 1.244 -.515 .075 24 26 45.280 -.582 1.008 1.182 5.739 -.005 .000 -.000 .003 -1.338 .580 -.088 25 14 33.549 1.363 4.216 -.438 2.139 .007 -.000 .000 -1.189 1.226 -.690 26 13 34.386 2.334 .553 .503 4.289 .158 -.018 .001 -.000 -.127 1.276 -.620 .114 27 3 2.753 .411 1.557 .733 2.893 -.011 .001 -.000 -1.511 .457 -.213 .038 28 9 17.041 2.413 1.222 .951 3.981 -.003 .000 -.000 -1.036 -.239 .038 .017 29 15 51.503 1.730 2.438 .073 2.108 -.003 .000 -.000 .821 .666 -.290 .040 30 15 52.229 -1.410 1.206 .280 2.178 -.003 .000 -.000 .275 -.707 .383 -.077 31 3 3.662 1.518 2.384 -.364 2.315 .008 -.000 .000 -.934 -1.291 .370 - 32 4 11.408 -.519 5.446 -.112 1.582 .014 -.003 .000 -.000 1.179 -.517 .306 -.065 33 7 13.980 .070 1.689 -.320 3.397 .006 -.000 .000

Table 1. Summary and diagnostic statistics for each discovered cluster. For each cluster, indexed by the first column, column 2 reports the number of members, while column 3 and 4 the parameters of the statistical model: residual sum of squares and regression coefficients. The last four columns report the statistics of standardized residuals for diagnostic purposes. For standardized residuals following approximatively a normal distribution, the mean should be close to 0, the standard deviation to 1, the skewness to 0 and Kurtosis to 3.

A critical aspect of statistical inference is to assess the goodness of fit of the learned model. In our case, diagnostic analysis of the statistical model is performed by checking the normality of the standardized residuals of each cluster. Cluster residuals are computed by rescaling the differences between the observed values and the values predicted by the model fitted for each cluster. The rescaling factor is the inter-cluster variability. A good fit produces residuals following approximatively a normal distribution with mean 0 and standard deviation 1. The last four columns of Table 1 report the descriptive statistics of the residuals of each cluster. For a sample from a normal distribution, skewness, a measure of asymmetry, should be close to 0 and Kurtosis close to 3. For small clusters , such as cluster 27, 28, 31, 32, 33, containing less than 10 series, deviance from these values may be due to the limited number of available residuals rather than departure from normality. Figure 4 draws the file:///C|/...ferential analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED.html[11/17/2009 1:43:24 PM] Isogenic Cell Lines Common Genes

distribution of the residuals for each cluster.

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Figure 4. Standardized residuals for each discovered cluster, used for diagnostic purposes. Standardized residuals are computed by rescaling the differences between the observed values and the values predicted by the model fitted for each cluster. Good fit should yield to normally distributed residuals. Click on the images to enlarge.

A complete list of the genes included in the analysis and their cluster assignment is available here.

References

1. Ramoni, MF, Sebastiani, P and Kohane IS (2002). Cluster Analysis of Gene Expression Dynamics. Under review. 2. Eisen, M, Spellman, P, Brown, P and Botstein, D (1998). Cluster analysis and display of genome-wide expression patterns, Proc Nat Acad Sci USA, 95:14863-14868.

This report was generated by CAGED v1.0.

file:///C|/...ferential analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED.html[11/17/2009 1:43:24 PM] List of All Genes

CAGED Report (November 17, 2009)

List of All Genes

Cluster Accession Number Description 1 NM_005415 SLC20A1 HER2 1 NM_004207 SLC16A3 HER2 1 NM_001823 CKB 10A 1 NM_006471 MRCL3 HER2 1 NM_020182 TMEPAI HER2 1 NM_006779 CDC42EP2 HER2 1 NM_015062 PPRC1 HER2 1 NM_000308 CTSA 10A 1 NM_004431 EPHA2 HER2 1 NM_001011 RPS7 10A 1 NM_152594 SPRED1 HER2 1 NM_002467 MYC HER2 1 NM_004688 NMI 10A 1 NM_016445 PLEK2 10A 1 NM_000574 CD55 HER2/E7 1 NM_015062 PPRC1 HER2/E7 1 NM_004454 ETV5 10A 1 NM_015201 BOP1 10A 1 NM_005789 PSME3 10A 1 NM_003739 AKR1C3 10A 1 NM_000713 BLVRB 10A 1 NM_003311 PHLDA2 10A 1 NM_030961 TRIM56 10A 1 NM_007112 THBS3 10A 1 NM_001954 DDR1 10A 2 NM_004089 TSC22D3 10A 2 NM_005896 IDH1 HER2/E7 2 NM_006437 PARP4 10A 2 NM_003204 NFE2L1 10A 2 NM_002415 MIF HER2 2 NM_003707 RUVBL1 10A 2 NM_006810 PDIA5 10A 2 NM_002792 PSMA7 10A 2 NM_001017430 RBM3 10A 2 NM_024698 SLC25A22 10A 2 NM_004207 SLC16A3 10A 2 NM_019102 HOXA5 10A 2 NM_001005474 NFKBIZ 10A 2 NM_006854 KDELR2 10A 2 NM_018100 EFHC1 10A 2 NM_003860 BANF1 10A 2 NM_002415 MIF HER2/E7 2 NM_138387 G6PC3 10A 2 NM_175617 MT1E HER2/E7 2 NM_012254 SLC27A5 HER2/E7 2 NM_014026 DCPS HER2/E7

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2 NM_001827 CKS2 HER2/E7 2 NM_033285 TP53INP1 10A 3 NM_030758 OSBP2 HER2 3 NM_006372 SYNCRIP HER2 3 NM_005130 FGFBP1 HER2 3 NM_004454 ETV5 HER2/E7 3 NM_001101 ACTB HER2/E7 3 NM_016639 TNFRSF12A 10A 3 NM_194281 C18orf37 HER2 3 NM_000428 LTBP2 HER2/E7 3 NM_182688 UBE2G2 HER2/E7 3 NM_003914 CCNA1 10A 3 NM_057175 NARG1 10A 3 NM_182688 UBE2G2 HER2 3 NM_175709 CBX7 10A 3 NM_015076 CDC2L6 10A 3 NM_004741 NOLC1 10A 3 NM_057158 DUSP4 10A 3 NM_002648 PIM1 10A 3 NM_194281 C18orf37 10A 3 NM_005796 NUTF2 HER2 3 NM_080607 C20orf102 10A 3 NM_002539 ODC1 10A 3 NM_006042 HS3ST3A1 10A 3 NM_004864 GDF15 HER2/E7 3 NM_000228 LAMB3 10A 3 NM_032485 MCM8 10A 3 NM_024039 MIS12 HER2/E7 3 NM_152594 SPRED1 HER2/E7 3 NM_138578 BCL2L1 HER2/E7 3 NM_024644 C14orf169 HER2 3 NM_014918 CHSY1 HER2 3 NM_000317 PTS HER2 3 NM_005243 EWSR1 HER2 3 NM_002936 RNASEH1 HER2 3 NM_005827 SLC35B1 HER2 3 NM_001278 CHUK HER2 3 NM_005789 PSME3 HER2 3 NM_000820 GAS6 10A 3 NM_000076 CDKN1C HER2 4 NM_003565 ULK1 10A 4 NM_004814 WDR57 HER2 4 NM_006114 TOMM40 HER2 4 NM_017421 COQ3 HER2 4 NM_013974 DDAH2 10A 4 NM_001008397 LOC493869 HER2 4 NM_020310 MNT 10A 4 NM_016306 DNAJB11 HER2 4 NM_138387 G6PC3 HER2 4 NM_018664 SNFT HER2 4 NM_005792 MPHOSPH6 HER2 4 NM_001986 ETV4 HER2 4 NM_198319 PRMT1 HER2 4 NM_005782 THOC4 HER2/E7 file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

4 NM_000270 NP HER2 4 NM_006216 SERPINE2 10A 4 NM_015934 NOP5/NOP58 HER2 4 NM_002845 PTPRM 10A 4 NM_000190 HMBS HER2 4 NM_001794 CDH4 10A 4 NM_032346 PDCD2L HER2 4 NM_006372 SYNCRIP HER2/E7 4 NM_213636 PDLIM7 HER2 4 NM_006170 NOL1 HER2 4 NM_025215 PUS1 HER2 4 NM_012280 FTSJ1 HER2 4 NM_005950 MT1G 10A 4 NM_024039 MIS12 HER2 4 NM_003404 YWHAB HER2 4 NM_003707 RUVBL1 HER2 4 NM_012459 TIMM8B HER2 4 NM_006824 EBNA1BP2 HER2 4 NM_014252 SLC25A15 HER2 4 NM_002882 RANBP1 HER2 4 NM_006824 EBNA1BP2 10A 4 NM_182688 UBE2G2 10A 4 NM_021626 SCPEP1 10A 4 NM_198175 NME1 10A 4 NM_001905 CTPS HER2 4 NM_133443 GPT2 HER2 5 NM_002454 MTRR HER2 5 NM_012456 TIMM10 HER2 5 NM_014165 C6orf66 HER2 5 NM_004085 TIMM8A HER2 5 NM_020230 PPAN HER2 5 NM_004053 BYSL HER2 5 NM_024698 SLC25A22 HER2 5 NM_002149 HPCAL1 HER2 5 NM_012341 GTPBP4 HER2 5 NM_199187 KRT18 10A 5 NM_021830 PEO1 HER2 5 NM_057175 NARG1 HER2 5 NM_000317 PTS HER2/E7 5 NM_004269 CRSP8 HER2 5 NM_006033 LIPG HER2 5 NM_022044 SDF2L1 HER2/E7 5 NM_198938 PTGES2 HER2 5 NM_004708 PDCD5 HER2 5 NM_006170 NOL1 HER2/E7 5 NM_016310 POLR3K HER2 5 NM_001102 ACTN1 HER2/E7 5 NM_003860 BANF1 HER2 5 NM_006938 SNRPD1 HER2 5 NM_016306 DNAJB11 HER2/E7 5 NM_001325 CSTF2 HER2 5 NM_003243 TGFBR3 10A 5 NM_001024666 SH3KBP1 10A 5 NM_001412 EIF1AX 10A

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5 NM_138689 PPP1R14B HER2 5 NM_003877 SOCS2 HER2 5 NM_004705 PRKRIR HER2 5 NM_032993 NOLA1 HER2 5 NM_000819 GART HER2 5 NM_004741 NOLC1 HER2 5 NM_199329 SLC43A3 HER2 5 NM_170784 MKKS HER2 5 NM_012124 CHORDC1 HER2 6 NM_002198 IRF1 10A 6 NM_198066 GNPNAT1 HER2/E7 6 NM_015939 CGI-09 HER2 6 NM_022366 TFB2M HER2 6 NM_012124 CHORDC1 HER2/E7 6 NM_006779 CDC42EP2 HER2/E7 6 NM_000270 NP HER2/E7 6 NM_004704 RRP9 HER2 6 NM_016310 POLR3K HER2/E7 6 NM_024644 C14orf169 HER2/E7 6 NM_001905 CTPS HER2/E7 6 NM_002454 MTRR HER2/E7 6 NM_006033 LIPG HER2/E7 6 NM_020182 TMEPAI HER2/E7 6 NM_022767 ISG20L1 HER2/E7 6 NM_002936 RNASEH1 HER2/E7 6 NM_012456 TIMM10 HER2/E7 6 NM_001826 CKS1B HER2/E7 6 NM_001278 CHUK HER2/E7 6 NM_006290 TNFAIP3 10A 6 NM_014918 CHSY1 HER2/E7 6 NM_006471 MRCL3 HER2/E7 6 NM_018361 AGPAT5 HER2/E7 6 NM_016077 PTRH2 HER2 6 NM_015939 CGI-09 HER2/E7 6 NM_199329 SLC43A3 HER2/E7 6 NM_133443 GPT2 HER2/E7 6 NM_001010924 C10orf38 HER2/E7 6 NM_004705 PRKRIR HER2/E7 6 NM_012474 UCK2 10A 6 NM_015420 WDSOF1 HER2/E7 6 NM_004870 MPDU1 HER2/E7 6 NM_002997 SDC1 HER2/E7 6 NM_005789 PSME3 HER2/E7 6 NM_000819 GART 10A 6 NM_005827 SLC35B1 HER2/E7 6 NM_003491 ARD1A HER2/E7 6 NM_002882 RANBP1 HER2/E7 6 NM_006393 NEBL 10A 6 NM_003680 YARS HER2 6 NM_017767 SLC39A4 HER2/E7 6 NM_012459 TIMM8B HER2/E7 6 NM_001549 IFIT3 10A 6 NM_006938 SNRPD1 HER2/E7 6 NM_001629 ALOX5AP HER2/E7 file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

6 NM_013986 EWSR1 HER2/E7 6 NM_004078 CSRP1 HER2/E7 6 NM_004780 TCEAL1 10A 6 NM_021203 SRPRB HER2/E7 6 NM_012280 FTSJ1 HER2/E7 6 NM_000317 PTS 10A 6 NM_015440 MTHFD1L 10A 6 NM_004814 WDR57 HER2/E7 6 NM_004085 TIMM8A HER2/E7 6 NM_003095 SNRPF HER2/E7 6 NM_001008397 LOC493869 HER2/E7 6 NM_003093 SNRPC HER2/E7 6 NM_003290 TPM4 HER2/E7 6 NM_138408 C6orf51 HER2/E7 6 NM_138387 G6PC3 HER2/E7 6 NM_000485 APRT HER2/E7 6 NM_005022 PFN1 HER2/E7 6 NM_003860 BANF1 HER2/E7 6 NM_000801 FKBP1A HER2/E7 6 NM_000270 NP 10A 6 NM_005742 PDIA6 HER2/E7 6 NM_004048 B2M 10A 6 NM_021830 PEO1 10A 6 NM_198938 PTGES2 HER2/E7 6 NM_002792 PSMA7 HER2/E7 6 NM_007208 MRPL3 HER2/E7 6 NM_006623 PHGDH HER2/E7 6 NM_005381 NCL HER2/E7 6 NM_006442 DRAP1 HER2/E7 6 NM_001905 CTPS 10A 6 NM_004177 STX3 10A 6 NM_004044 ATIC HER2/E7 6 NM_002160 TNC HER2/E7 6 NM_001017430 RBM3 HER2/E7 6 NM_001325 CSTF2 HER2/E7 6 NM_014226 RAGE HER2/E7 6 NM_000532 PCCB HER2/E7 6 NM_003877 SOCS2 HER2/E7 6 NM_016292 TRAP1 HER2/E7 6 NM_004428 EFNA1 10A 6 NM_017767 SLC39A4 10A 6 NM_004577 PSPH 10A 6 NM_013319 UBIAD1 HER2 6 NM_015440 MTHFD1L HER2/E7 6 NM_015414 RPL36 HER2/E7 6 NM_001003796 NHP2L1 HER2/E7 6 NM_002949 MRPL12 HER2/E7 6 NM_005796 NUTF2 HER2/E7 6 NM_148173 PEMT HER2/E7 6 NM_012341 GTPBP4 HER2/E7 6 NM_000320 QDPR HER2/E7 6 NM_006703 NUDT3 HER2/E7 6 NM_004577 PSPH HER2/E7 6 NM_004708 PDCD5 HER2/E7

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6 NM_013319 UBIAD1 HER2/E7 6 NM_015934 NOP5/NOP58 HER2/E7 6 NM_032830 CIRH1A HER2/E7 6 NM_014366 GNL3 HER2/E7 6 NM_022366 TFB2M HER2/E7 6 NM_001363 DKC1 HER2/E7 6 NM_016498 MTP18 HER2/E7 6 NM_014038 BZW2 HER2/E7 6 NM_006191 PA2G4 HER2/E7 6 NM_017816 LYAR 10A 6 NM_000819 GART HER2/E7 6 NM_018188 ATAD3A HER2/E7 6 NM_003707 RUVBL1 HER2/E7 6 NM_004741 NOLC1 HER2/E7 6 NM_004728 DDX21 HER2/E7 6 NM_024698 SLC25A22 HER2/E7 6 NM_020230 PPAN HER2/E7 6 NM_025215 PUS1 HER2/E7 6 NM_014165 C6orf66 HER2/E7 6 NM_021830 PEO1 HER2/E7 6 NM_194281 C18orf37 HER2/E7 6 NM_006114 TOMM40 HER2/E7 6 NM_004417 DUSP1 10A 6 NM_199187 KRT18 HER2/E7 6 NM_004704 RRP9 HER2/E7 6 NM_001444 FABP5 HER2/E7 6 NM_014501 UBE2S HER2/E7 6 NM_032346 PDCD2L HER2/E7 6 NM_057175 NARG1 HER2/E7 6 NM_016077 PTRH2 HER2/E7 6 NM_194247 HNRPA3 HER2/E7 6 NM_001003684 UCRC HER2/E7 6 NM_170784 MKKS HER2/E7 6 NM_198830 ACLY HER2/E7 6 NM_014317 PDSS1 HER2/E7 6 NM_004053 BYSL HER2/E7 6 NM_004269 CRSP8 HER2/E7 6 NM_001412 EIF1AX HER2/E7 6 NM_001325 CSTF2 10A 6 NM_005080 XBP1 HER2/E7 6 NM_005792 MPHOSPH6 HER2/E7 7 NM_003311 PHLDA2 HER2/E7 7 NM_181353 ID1 HER2/E7 7 NM_002149 HPCAL1 HER2/E7 7 NM_032331 MGC2408 HER2/E7 7 NM_032993 NOLA1 HER2/E7 7 NM_030758 OSBP2 HER2/E7 7 NM_000071 CBS HER2/E7 7 NM_003680 YARS HER2/E7 7 NM_014366 GNL3 HER2 7 NM_015420 WDSOF1 HER2 7 NM_014317 PDSS1 HER2 7 NM_004095 EIF4EBP1 HER2/E7 7 NM_017767 SLC39A4 HER2 file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

7 NM_153824 PYCR1 HER2/E7 7 NM_002638 PI3 HER2/E7 7 NM_198175 NME1 HER2/E7 7 NM_002949 MRPL12 HER2 7 NM_003132 SRM HER2 7 NM_006002 UCHL3 HER2/E7 7 NM_016498 MTP18 HER2 7 NM_138408 C6orf51 HER2 7 NM_007208 MRPL3 HER2 7 NM_005833 RABEPK HER2 7 NM_013300 C12orf24 HER2 7 NM_003831 RIOK3 10A 7 NM_002527 NTF3 10A 7 NM_213636 PDLIM7 HER2/E7 7 NM_000676 ADORA2B HER2/E7 7 NM_001033059 AMD1 HER2/E7 7 NM_005415 SLC20A1 HER2/E7 7 NM_000076 CDKN1C 10A 7 NM_013300 C12orf24 HER2/E7 7 NM_017816 LYAR HER2/E7 7 NM_006042 HS3ST3A1 HER2/E7 7 NM_002161 IARS HER2/E7 7 NM_003132 SRM HER2/E7 7 NM_006854 KDELR2 HER2/E7 7 NM_006703 NUDT3 HER2 7 NM_003095 SNRPF HER2 7 NM_001024666 SH3KBP1 HER2/E7 7 NM_012254 SLC27A5 HER2 7 NM_020158 EXOSC5 HER2/E7 7 NM_012474 UCK2 HER2/E7 7 NM_003404 YWHAB HER2/E7 7 NM_174889 NDUFA12L HER2/E7 7 NM_001025242 IRAK1 HER2/E7 7 NM_015201 BOP1 HER2/E7 7 NM_001212 C1QBP HER2/E7 7 NM_000666 ACY1 HER2/E7 7 NM_198319 PRMT1 HER2/E7 7 NM_080820 DTD1 HER2/E7 7 NM_021121 EEF1B2 HER2/E7 7 NM_000190 HMBS HER2/E7 7 NM_003823 TNFRSF6B HER2/E7 7 NM_014252 SLC25A15 HER2/E7 7 NM_018188 ATAD3A HER2 7 NM_005833 RABEPK HER2/E7 7 NM_005805 PSMD14 HER2/E7 7 NM_138689 PPP1R14B HER2/E7 7 NM_001212 C1QBP HER2 7 NM_016445 PLEK2 HER2/E7 7 NM_006191 PA2G4 HER2 7 NM_005628 SLC1A5 HER2/E7 7 NM_018664 SNFT HER2/E7 7 NM_003914 CCNA1 HER2/E7 7 NM_000676 ADORA2B HER2 7 NM_003670 BHLHB2 HER2/E7

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

7 NM_000228 LAMB3 HER2/E7 8 NM_005782 THOC4 HER2 8 NM_001033059 AMD1 HER2 8 NM_003486 SLC7A5 HER2 8 NM_012474 UCK2 HER2 8 NM_006824 EBNA1BP2 HER2/E7 8 NM_002539 ODC1 HER2/E7 8 NM_006442 DRAP1 HER2 8 NM_004990 MARS HER2/E7 8 NM_001363 DKC1 HER2 8 NM_003823 TNFRSF6B HER2 8 NM_005805 PSMD14 HER2 8 NM_004577 PSPH HER2 8 NM_198066 GNPNAT1 HER2 8 NM_004728 DDX21 HER2 8 NM_004044 ATIC 10A 8 NM_004454 ETV5 HER2 8 NM_002997 SDC1 HER2 8 NM_001794 CDH4 HER2/E7 8 NM_014501 UBE2S HER2 8 NM_181597 UPP1 HER2/E7 8 NM_003311 PHLDA2 HER2 8 NM_005080 XBP1 HER2 8 NM_017816 LYAR HER2 8 NM_006022 TSC22D1 HER2 8 NM_012456 TIMM10 10A 8 NM_139314 ANGPTL4 HER2 9 NM_019102 HOXA5 HER2 9 NM_080607 C20orf102 HER2/E7 9 NM_005833 RABEPK 10A 9 NM_001455 FOXO3A HER2 9 NM_014343 CLDN15 HER2 9 NM_000396 CTSK HER2 9 NM_002386 MC1R HER2 9 NM_004117 FKBP5 HER2/E7 9 NM_001146 ANGPT1 HER2/E7 9 NM_000713 BLVRB HER2 9 NM_019600 KIAA1370 HER2 9 NM_016621 PHF21A HER2/E7 9 NM_000755 CRAT 10A 9 NM_006454 MXD4 HER2/E7 9 NM_006393 NEBL HER2 9 NM_006195 PBX3 HER2 9 NM_005589 ALDH6A1 HER2 9 NM_015439 CCDC28A HER2 9 NM_006268 DPF2 HER2 9 NM_037370 CCNDBP1 HER2 9 NM_015076 CDC2L6 HER2 9 NM_176878 INADL 10A 9 NM_001165 BIRC3 10A 9 NM_001003684 UCRC 10A 9 NM_006328 RBM14 HER2/E7 9 NM_004870 MPDU1 10A 9 NM_006372 SYNCRIP 10A file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

9 NM_003819 PABPC4 HER2/E7 9 NM_001018109 PIR HER2/E7 9 NM_198066 GNPNAT1 10A 9 NM_000532 PCCB 10A 9 NM_024644 C14orf169 10A 9 NM_013974 DDAH2 HER2/E7 9 NM_001307 CLDN7 HER2/E7 9 NM_005204 MAP3K8 HER2/E7 9 NM_003831 RIOK3 HER2/E7 9 NM_004772 C5orf13 HER2/E7 10 NM_001278 CHUK 10A 10 NM_002166 ID2 10A 10 NM_002583 PAWR HER2/E7 10 NM_003831 RIOK3 HER2 10 NM_025194 ITPKC HER2/E7 10 NM_018188 ATAD3A 10A 10 NM_000701 ATP1A1 HER2/E7 10 NM_002778 PSAP 10A 10 NM_006191 PA2G4 10A 10 NM_004990 MARS 10A 10 NM_001002236 SERPINA1 10A 10 NM_001629 ALOX5AP 10A 10 NM_022168 IFIH1 10A 10 NM_004669 CLIC3 HER2/E7 10 NM_015374 UNC84B 10A 10 NM_000701 ATP1A1 HER2 10 NM_001312 CRIP2 10A 10 NM_004240 TRIP10 HER2 10 NM_004512 IL11RA 10A 10 NM_004431 EPHA2 10A 10 NM_002636 PHF1 HER2 10 NM_005796 NUTF2 10A 10 NM_002964 S100A8 HER2/E7 10 NM_003331 TYK2 10A 10 NM_013319 UBIAD1 10A 10 NM_000336 SCNN1B 10A 10 NM_002526 NT5E 10A 10 NM_014343 CLDN15 10A 10 NM_004559 YBX1 10A 10 NM_006114 TOMM40 10A 10 NM_012257 HBP1 10A 10 NM_006170 NOL1 10A 10 NM_022044 SDF2L1 10A 10 NM_006379 SEMA3C 10A 10 NM_001124 ADM HER2 10 NM_001630 ANXA8 HER2/E7 10 NM_005557 KRT16 HER2 10 NM_006779 CDC42EP2 10A 10 NM_001005619 ITGB4 HER2 10 NM_174889 NDUFA12L 10A 10 NM_199246 CCNG1 HER2 10 NM_003819 PABPC4 HER2 10 NM_000574 CD55 HER2 11 NM_175047 PILRB HER2

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

11 NM_003793 CTSF HER2 11 NM_005115 MVP HER2 11 NM_005764 PDZK1IP1 HER2/E7 11 NM_021034 IFITM3 HER2/E7 11 NM_005319 HIST1H1C HER2/E7 11 NM_001024646 CLK1 HER2/E7 11 NM_005792 MPHOSPH6 10A 11 NM_004666 VNN1 HER2/E7 11 NM_018973 DPM3 HER2/E7 11 NM_002557 OVGP1 HER2/E7 11 NM_001995 ACSL1 HER2/E7 11 NM_007112 THBS3 HER2/E7 11 NM_032432 ABLIM2 HER2 11 NM_022121 PERP HER2 11 NM_006320 PGRMC2 HER2 11 NM_002957 RXRA HER2/E7 11 NM_175709 CBX7 HER2/E7 11 NM_000308 CTSA HER2 11 NM_020158 EXOSC5 10A 11 NM_020898 CALCOCO1 HER2/E7 11 NM_003407 ZFP36 HER2/E7 11 NM_133491 SAT2 HER2/E7 11 NM_003204 NFE2L1 HER2/E7 11 NM_020898 CALCOCO1 10A 11 NM_018031 WDR6 HER2 11 NM_021034 IFITM3 10A 11 NM_002087 GRN HER2 11 NM_002778 PSAP HER2/E7 11 NM_012341 GTPBP4 10A 11 NM_176096 CDK5RAP3 HER2 11 NM_007112 THBS3 HER2 11 NM_013986 EWSR1 10A 11 NM_003879 CFLAR HER2/E7 11 NM_005596 NFIB HER2/E7 11 NM_006486 FBLN1 HER2/E7 11 NM_001008212 OPTN HER2/E7 11 NM_003879 CFLAR HER2 11 NM_001165 BIRC3 HER2 11 NM_022168 IFIH1 HER2 11 NM_014317 PDSS1 10A 11 NM_014501 UBE2S 10A 11 NM_000320 QDPR 10A 11 NM_000196 HSD11B2 10A 11 NM_001212 C1QBP 10A 11 NM_001632 ALPP HER2 11 NM_176878 INADL HER2 11 NM_000916 OXTR 10A 11 NM_018664 SNFT 10A 11 NM_181785 LOC283537 HER2/E7 11 NM_018368 LMBRD1 HER2/E7 11 NM_021203 SRPRB 10A 11 NM_001031806 ALDH3A2 HER2/E7 11 NM_012434 SLC17A5 HER2 11 NM_002844 PTPRK HER2 file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

11 NM_020244 CHPT1 HER2/E7 12 NM_001032386 SUOX HER2/E7 12 NM_006874 ELF2 HER2 12 NM_002870 RAB13 HER2 12 NM_012257 HBP1 HER2/E7 12 NM_006493 CLN5 HER2 12 NM_002844 PTPRK HER2/E7 12 NM_033405 PRIC285 HER2/E7 12 NM_001005474 NFKBIZ HER2/E7 12 NM_012257 HBP1 HER2 12 NM_021260 ZFYVE1 HER2 12 NM_005667 RNF103 HER2 12 NM_021260 ZFYVE1 HER2/E7 12 NM_015439 CCDC28A HER2/E7 12 NM_002467 MYC 10A 12 NM_033285 TP53INP1 HER2/E7 12 NM_019600 KIAA1370 HER2/E7 12 NM_003670 BHLHB2 10A 12 NM_032331 MGC2408 10A 12 NM_005195 CEBPD 10A 12 NM_005667 RNF103 HER2/E7 12 NM_000308 CTSA HER2/E7 12 NM_002198 IRF1 HER2/E7 12 NM_003917 AP1G2 HER2/E7 12 NM_018031 WDR6 HER2/E7 12 NM_006320 PGRMC2 HER2/E7 12 NM_175875 SIX5 HER2/E7 12 NM_020247 CABC1 HER2/E7 12 NM_007233 TP53AP1 HER2/E7 12 NM_020196 XAB2 HER2/E7 12 NM_003331 TYK2 HER2/E7 12 NM_004048 B2M HER2/E7 12 NM_006195 PBX3 HER2/E7 12 NM_018973 DPM3 HER2 12 NM_012434 SLC17A5 HER2/E7 12 NM_006874 ELF2 HER2/E7 12 NM_004148 NINJ1 HER2/E7 12 NM_001885 CRYAB 10A 12 NM_004688 NMI HER2 12 NM_004780 TCEAL1 HER2/E7 12 NM_037370 CCNDBP1 HER2/E7 12 NM_007233 TP53AP1 10A 12 NM_022168 IFIH1 HER2/E7 12 NM_000701 ATP1A1 10A 12 NM_006493 CLN5 HER2/E7 12 NM_001549 IFIT3 HER2/E7 12 NM_002636 PHF1 HER2/E7 12 NM_004240 TRIP10 HER2/E7 12 NM_003127 SPTAN1 HER2/E7 12 NM_181869 APAF1 HER2/E7 12 NM_006268 DPF2 HER2/E7 12 NM_002868 RAB5B HER2/E7 12 NM_002386 MC1R HER2/E7 12 NM_005628 SLC1A5 10A

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

12 NM_001007069 SDCBP HER2/E7 12 NM_199246 CCNG1 HER2/E7 12 NM_015076 CDC2L6 HER2/E7 12 NM_006437 PARP4 HER2/E7 12 NM_004688 NMI HER2/E7 12 NM_006876 B3GNT1 HER2/E7 12 NM_032812 PLXDC2 HER2/E7 12 NM_175875 SIX5 HER2 12 NM_000391 TPP1 HER2 12 NM_006320 PGRMC2 10A 12 NM_001032386 SUOX HER2 12 NM_018011 FLJ10154 10A 12 NM_181869 APAF1 HER2 12 NM_002868 RAB5B HER2 12 NM_033285 TP53INP1 HER2 12 NM_003331 TYK2 HER2 12 NM_006437 PARP4 HER2 13 NM_025215 PUS1 10A 13 NM_002053 GBP1 10A 13 NM_000422 KRT17 10A 13 NM_002845 PTPRM HER2 13 NM_005805 PSMD14 10A 13 NM_005516 HLA-E HER2 13 NM_015439 CCDC28A 10A 13 NM_000755 CRAT HER2 13 NM_014454 SESN1 10A 13 NM_001706 BCL6 10A 13 NM_005130 FGFBP1 10A 13 NM_004628 XPC 10A 13 NM_005742 PDIA6 10A 13 NM_153824 PYCR1 10A 13 NM_005978 S100A2 10A 13 NM_004704 RRP9 10A 13 NM_001146 ANGPT1 10A 13 NM_181869 APAF1 10A 13 NM_176096 CDK5RAP3 10A 13 NM_021260 ZFYVE1 10A 13 NM_000691 ALDH3A1 10A 13 NM_018361 AGPAT5 10A 13 NM_032432 ABLIM2 10A 13 NM_006623 PHGDH 10A 13 NM_014226 RAGE 10A 13 NM_005080 XBP1 10A 13 NM_020428 SLC44A2 10A 13 NM_031412 GABARAPL1 10A 13 NM_002178 IGFBP6 10A 13 NM_213636 PDLIM7 10A 13 NM_006002 UCHL3 10A 13 NM_003806 HRK 10A 13 NM_005764 PDZK1IP1 10A 13 NM_181782 NCOA7 10A 13 NM_005516 HLA-E HER2/E7 13 NM_002870 RAB13 HER2/E7 13 NM_134426 SLC26A6 10A file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

13 NM_014165 C6orf66 10A 13 NM_000485 APRT 10A 13 NM_020353 PLSCR4 10A 13 NM_012254 SLC27A5 10A 13 NM_002970 SAT1 HER2/E7 13 NM_001002857 ANXA2 10A 13 NM_014266 HCST 10A 13 NM_006938 SNRPD1 10A 13 NM_020310 MNT HER2/E7 13 NM_000713 BLVRB HER2/E7 13 NM_020244 CHPT1 10A 13 NM_000428 LTBP2 10A 13 NM_014038 BZW2 10A 13 NM_015062 PPRC1 10A 13 NM_003093 SNRPC 10A 13 NM_138578 BCL2L1 HER2 13 NM_004207 SLC16A3 HER2/E7 13 NM_057158 DUSP4 HER2/E7 13 NM_199246 CCNG1 10A 13 NM_006442 DRAP1 10A 13 NM_006290 TNFAIP3 HER2/E7 13 NM_003407 ZFP36 HER2 13 NM_003290 TPM4 10A 13 NM_002423 MMP7 10A 13 NM_194247 HNRPA3 10A 13 NM_002161 IARS 10A 13 NM_002583 PAWR HER2 13 NM_015939 CGI-09 10A 13 NM_020196 XAB2 HER2 13 NM_133443 GPT2 10A 13 NM_002527 NTF3 HER2 13 NM_020310 MNT HER2 13 NM_032121 RP11-217H1.1 HER2 13 NM_004603 STX1A HER2 13 NM_005557 KRT16 HER2/E7 13 NM_006509 RELB HER2/E7 14 NM_006195 PBX3 10A 14 NM_032485 MCM8 HER2 14 NM_018561 USP49 HER2 14 NM_002149 HPCAL1 10A 14 NM_032346 PDCD2L 10A 14 NM_001630 ANXA8 10A 14 NM_006493 CLN5 10A 14 NM_001039 SCNN1G 10A 14 NM_004240 TRIP10 10A 14 NM_000820 GAS6 HER2/E7 14 NM_012434 SLC17A5 10A 14 NM_006509 RELB 10A 14 NM_002166 ID2 HER2/E7 14 NM_001547 IFIT2 10A 14 NM_020376 PNPLA2 10A 14 NM_002636 PHF1 10A 14 NM_001444 FABP5 10A 14 NM_003500 ACOX2 10A

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

14 NM_001363 DKC1 10A 14 NM_080797 DIDO1 HER2 14 NM_005410 SEPP1 10A 14 NM_019600 KIAA1370 10A 14 NM_003132 SRM 10A 14 NM_002053 GBP1 HER2/E7 14 NM_000676 ADORA2B 10A 14 NM_005410 SEPP1 HER2/E7 14 NM_015044 GGA2 HER2/E7 14 NM_002845 PTPRM HER2/E7 14 NM_004603 STX1A HER2/E7 14 NM_000196 HSD11B2 HER2/E7 14 NM_004177 STX3 HER2/E7 14 NM_003806 HRK HER2/E7 14 NM_006703 NUDT3 10A 14 NM_001032386 SUOX 10A 14 NM_020998 MST1 10A 14 NM_004078 CSRP1 10A 14 NM_001547 IFIT2 HER2/E7 14 NM_004085 TIMM8A 10A 14 NM_003512 HIST1H2AC 10A 14 NM_001101 ACTB 10A 14 NM_002386 MC1R 10A 14 NM_004772 C5orf13 10A 14 NM_005415 SLC20A1 10A 14 NM_015420 WDSOF1 10A 14 NM_002658 PLAU 10A 14 NM_005589 ALDH6A1 10A 14 NM_004628 XPC HER2/E7 14 NM_003917 AP1G2 10A 14 NM_018100 EFHC1 HER2/E7 14 NM_018368 LMBRD1 10A 14 NM_020529 NFKBIA 10A 14 NM_007146 VEZF1 HER2/E7 14 NM_004512 IL11RA HER2/E7 14 NM_000391 TPP1 HER2/E7 14 NM_001008397 LOC493869 10A 14 NM_015274 MAN2B2 HER2/E7 14 NM_175047 PILRB HER2/E7 14 NM_001954 DDR1 HER2/E7 14 NM_002578 PAK3 HER2/E7 14 NM_176878 INADL HER2/E7 14 NM_001124 ADM HER2/E7 14 NM_000396 CTSK HER2/E7 14 NM_134426 SLC26A6 HER2/E7 14 NM_080797 DIDO1 HER2/E7 14 NM_176096 CDK5RAP3 HER2/E7 14 NM_030961 TRIM56 HER2/E7 14 NM_002957 RXRA 10A 14 NM_015374 UNC84B HER2/E7 14 NM_001986 ETV4 10A 14 NM_004095 EIF4EBP1 10A 14 NM_013300 C12orf24 10A 14 NM_018011 FLJ10154 HER2/E7 file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

14 NM_003486 SLC7A5 10A 14 NM_004864 GDF15 10A 14 NM_002415 MIF 10A 14 NM_001005619 ITGB4 10A 14 NM_152227 SNX5 10A 14 NM_002882 RANBP1 10A 14 NM_020230 PPAN 10A 14 NM_032121 RP11-217H1.1 HER2/E7 14 NM_032485 MCM8 HER2/E7 14 NM_018561 USP49 HER2/E7 14 NM_001632 ALPP HER2/E7 14 NM_003512 HIST1H2AC HER2/E7 14 NM_019102 HOXA5 HER2/E7 14 NM_014026 DCPS 10A 14 NM_001885 CRYAB HER2/E7 14 NM_005896 IDH1 HER2 14 NM_001025242 IRAK1 10A 14 NM_015044 GGA2 HER2 14 NM_002949 MRPL12 10A 14 NM_021991 JUP 10A 14 NM_004048 B2M HER2 14 NM_004177 STX3 HER2 14 NM_002870 RAB13 10A 14 NM_001008540 CXCR4 10A 14 NM_030961 TRIM56 HER2 14 NM_003127 SPTAN1 HER2 14 NM_018011 FLJ10154 HER2 14 NM_014343 CLDN15 HER2/E7 14 NM_032121 RP11-217H1.1 10A 14 NM_001101 ACTB HER2 14 NM_001024646 CLK1 10A 14 NM_001632 ALPP 10A 14 NM_007146 VEZF1 HER2 14 NM_004814 WDR57 10A 14 NM_018561 USP49 10A 14 NM_016621 PHF21A 10A 14 NM_181353 ID1 10A 14 NM_000990 RPL27A HER2/E7 14 NM_001102 ACTN1 10A 14 NM_005557 KRT16 10A 14 NM_037370 CCNDBP1 10A 14 NM_005022 PFN1 10A 14 NM_000428 LTBP2 HER2 14 NM_002578 PAK3 10A 14 NM_030754 SAA2 HER2/E7 15 NM_001986 ETV4 HER2/E7 15 NM_000801 FKBP1A HER2 15 NM_005516 HLA-E 10A 15 NM_175617 MT1E HER2 15 NM_003093 SNRPC HER2 15 NM_175047 PILRB 10A 15 NM_012459 TIMM8B 10A 15 NM_001444 FABP5 HER2 15 NM_004870 MPDU1 HER2

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

15 NM_003819 PABPC4 10A 15 NM_005419 STAT2 10A 15 NM_080820 DTD1 HER2 15 NM_001025242 IRAK1 HER2 15 NM_001323 CST6 10A 15 NM_004044 ATIC HER2 15 NM_139314 ANGPTL4 10A 15 NM_002997 SDC1 10A 15 NM_014918 CHSY1 10A 15 NM_003404 YWHAB 10A 15 NM_000190 HMBS 10A 15 NM_000391 TPP1 10A 15 NM_198319 PRMT1 10A 15 NM_000666 ACY1 10A 15 NM_006876 B3GNT1 10A 15 NM_080797 DIDO1 10A 15 NM_020247 CABC1 10A 15 NM_005319 HIST1H1C 10A 15 NM_198938 PTGES2 10A 15 NM_017421 COQ3 10A 15 NM_006328 RBM14 10A 15 NM_016310 POLR3K 10A 15 NM_012124 CHORDC1 10A 15 NM_138408 C6orf51 10A 15 NM_001010924 C10orf38 10A 15 NM_005667 RNF103 10A 15 NM_016077 PTRH2 10A 15 NM_005827 SLC35B1 10A 15 NM_001033059 AMD1 10A 15 NM_001003796 NHP2L1 10A 15 NM_003823 TNFRSF6B 10A 15 NM_001024465 SOD2 10A 15 NM_181785 LOC283537 10A 15 NM_003313 TSTA3 10A 15 NM_175875 SIX5 10A 15 NM_021154 PSAT1 10A 15 NM_170784 MKKS 10A 15 NM_031286 SH3BGRL3 HER2 15 NM_133491 SAT2 10A 15 NM_138689 PPP1R14B 10A 15 NM_003407 ZFP36 10A 15 NM_005782 THOC4 10A 15 NM_002160 TNC HER2 15 NM_018031 WDR6 10A 15 NM_017671 C20orf42 10A 15 NM_002936 RNASEH1 10A 15 NM_001002857 ANXA2 HER2 15 NM_000320 QDPR HER2 15 NM_006079 CITED2 10A 15 NM_004148 NINJ1 10A 15 NM_002792 PSMA7 HER2 15 NM_001412 EIF1AX HER2 15 NM_001826 CKS1B 10A 15 NM_148173 PEMT 10A file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

15 NM_080820 DTD1 10A 15 NM_004728 DDX21 10A 15 NM_006022 TSC22D1 HER2/E7 15 NM_004431 EPHA2 HER2/E7 15 NM_002658 PLAU HER2/E7 15 NM_000916 OXTR HER2/E7 15 NM_016639 TNFRSF12A HER2/E7 15 NM_003633 ENC1 HER2/E7 15 NM_000916 OXTR HER2 16 NM_006268 DPF2 10A 16 NM_194247 HNRPA3 HER2 16 NM_003491 ARD1A HER2 16 NM_014252 SLC25A15 10A 16 NM_002454 MTRR 10A 16 NM_005742 PDIA6 HER2 16 NM_001003684 UCRC HER2 16 NM_001003796 NHP2L1 HER2 16 NM_015414 RPL36 HER2 16 NM_017421 COQ3 HER2/E7 16 NM_198830 ACLY 10A 16 NM_000485 APRT HER2 16 NM_003500 ACOX2 HER2/E7 16 NM_014366 GNL3 10A 16 NM_002583 PAWR 10A 16 NM_000990 RPL27A 10A 16 NM_148173 PEMT HER2 16 NM_016306 DNAJB11 10A 16 NM_001307 CLDN7 10A 16 NM_004559 YBX1 HER2/E7 16 NM_014026 DCPS HER2 16 NM_004705 PRKRIR 10A 16 NM_005130 FGFBP1 HER2/E7 16 NM_005896 IDH1 10A 16 NM_152594 SPRED1 10A 16 NM_004559 YBX1 HER2 16 NM_007146 VEZF1 10A 16 NM_133436 ASNS 10A 16 NM_001018109 PIR 10A 16 NM_181597 UPP1 10A 16 NM_015414 RPL36 10A 16 NM_005204 MAP3K8 10A 16 NM_015044 GGA2 10A 16 NM_021121 EEF1B2 10A 16 NM_003095 SNRPF 10A 16 NM_004666 VNN1 10A 16 NM_003680 YARS 10A 16 NM_002638 PI3 10A 16 NM_016498 MTP18 10A 16 NM_018361 AGPAT5 HER2 16 NM_003313 TSTA3 HER2 16 NM_006854 KDELR2 HER2 16 NM_002964 S100A8 10A 17 NM_005204 MAP3K8 HER2 17 NM_002166 ID2 HER2

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

17 NM_005115 MVP 10A 17 NM_134426 SLC26A6 HER2 17 NM_133491 SAT2 HER2 17 NM_007233 TP53AP1 HER2 17 NM_002957 RXRA HER2 17 NM_001630 ANXA8 HER2 17 NM_054014 FKBP1A 10A 17 NM_004445 EPHB6 HER2/E7 17 NM_000755 CRAT HER2/E7 17 NM_014266 HCST HER2 17 NM_022121 PERP 10A 17 NM_002087 GRN HER2/E7 17 NM_003879 CFLAR 10A 17 NM_001018 RPS15 10A 17 NM_002868 RAB5B 10A 17 NM_025194 ITPKC HER2 17 NM_001024646 CLK1 HER2 17 NM_004628 XPC HER2 17 NM_080607 C20orf102 HER2 17 NM_001954 DDR1 HER2 17 NM_000071 CBS 10A 17 NM_003917 AP1G2 HER2 17 NM_018100 EFHC1 HER2 17 NM_014266 HCST HER2/E7 17 NM_022121 PERP HER2/E7 17 NM_002557 OVGP1 HER2 17 NM_021991 JUP HER2/E7 17 NM_001455 FOXO3A HER2/E7 17 NM_031412 GABARAPL1 HER2 17 NM_181782 NCOA7 HER2/E7 17 NM_005589 ALDH6A1 HER2/E7 17 NM_005596 NFIB HER2 17 NM_020428 SLC44A2 HER2/E7 17 NM_018368 LMBRD1 HER2 17 NM_175709 CBX7 HER2 17 NM_005115 MVP HER2/E7 17 NM_148177 FBXO32 10A 17 NM_015934 NOP5/NOP58 10A 17 NM_001124 ADM 10A 17 NM_032812 PLXDC2 HER2 17 NM_004780 TCEAL1 HER2 17 NM_020353 PLSCR4 HER2 17 NM_003512 HIST1H2AC HER2 17 NM_001005474 NFKBIZ HER2 17 NM_014454 SESN1 HER2/E7 17 NM_004428 EFNA1 HER2/E7 17 NM_001823 CKB HER2 17 NM_018719 CDCA7L HER2 17 NM_006006 ZBTB16 HER2 17 NM_003739 AKR1C3 HER2/E7 18 NM_018719 CDCA7L HER2/E7 18 NM_020898 CALCOCO1 HER2 18 NM_020998 MST1 HER2 18 NM_021991 JUP HER2 file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

18 NM_020998 MST1 HER2/E7 18 NM_001885 CRYAB HER2 18 NM_004417 DUSP1 HER2/E7 18 NM_020353 PLSCR4 HER2/E7 18 NM_005419 STAT2 HER2/E7 18 NM_145693 LPIN1 HER2/E7 18 NM_021626 SCPEP1 HER2/E7 18 NM_003793 CTSF HER2/E7 18 NM_003565 ULK1 HER2 18 NM_000691 ALDH3A1 HER2/E7 18 NM_020529 NFKBIA HER2/E7 18 NM_145693 LPIN1 HER2 18 NM_006393 NEBL HER2/E7 18 NM_020376 PNPLA2 HER2/E7 18 NM_001823 CKB HER2/E7 18 NM_052880 MGC17330 HER2/E7 18 NM_003565 ULK1 HER2/E7 18 NM_006006 ZBTB16 HER2/E7 18 NM_031412 GABARAPL1 HER2/E7 18 NM_002648 PIM1 HER2/E7 18 NM_001731 BTG1 HER2/E7 18 NM_002778 PSAP HER2 18 NM_005195 CEBPD HER2/E7 18 NM_003243 TGFBR3 HER2/E7 18 NM_006379 SEMA3C HER2/E7 18 NM_001165 BIRC3 HER2/E7 18 NM_001706 BCL6 HER2/E7 18 NM_006454 MXD4 HER2 18 NM_001008540 CXCR4 HER2/E7 18 NM_052880 MGC17330 HER2 18 NM_004089 TSC22D3 HER2/E7 18 NM_138720 HIST1H2BD HER2 18 NM_002844 PTPRK 10A 18 NM_004666 VNN1 HER2 18 NM_003516 HIST2H2AA3 HER2/E7 18 NM_001024465 SOD2 HER2/E7 18 NM_001005619 ITGB4 HER2/E7 18 NM_001024465 SOD2 HER2 18 NM_030758 OSBP2 10A 18 NM_001312 CRIP2 HER2 18 NM_032432 ABLIM2 HER2/E7 18 NM_007021 C10orf10 HER2/E7 19 NM_001323 CST6 HER2 19 NM_005022 PFN1 HER2 19 NM_003491 ARD1A 10A 19 NM_022044 SDF2L1 HER2 19 NM_004095 EIF4EBP1 HER2 19 NM_001827 CKS2 HER2 19 NM_003254 TIMP1 HER2/E7 19 NM_021121 EEF1B2 HER2 19 NM_000071 CBS HER2 19 NM_006002 UCHL3 HER2 19 NM_006810 PDIA5 HER2 19 NM_002087 GRN 10A

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

19 NM_000574 CD55 10A 19 NM_001731 BTG1 10A 19 NM_006216 SERPINE2 HER2 19 NM_004117 FKBP5 10A 19 NM_004269 CRSP8 10A 19 NM_030754 SAA2 10A 19 NM_138720 HIST1H2BD 10A 20 NM_022767 ISG20L1 10A 20 NM_006216 SERPINE2 HER2/E7 20 NM_001017430 RBM3 HER2 20 NM_000228 LAMB3 HER2 20 NM_001002236 SERPINA1 HER2 20 NM_014038 BZW2 HER2 20 NM_006810 PDIA5 HER2/E7 20 NM_002178 IGFBP6 HER2 20 NM_018719 CDCA7L 10A 20 NM_016292 TRAP1 HER2 20 NM_005381 NCL HER2 20 NM_199187 KRT18 HER2 20 NM_025194 ITPKC 10A 20 NM_001455 FOXO3A 10A 20 NM_031286 SH3BGRL3 10A 20 NM_001002236 SERPINA1 HER2/E7 20 NM_013269 CLEC2D HER2/E7 20 NM_003313 TSTA3 HER2/E7 20 NM_001031806 ALDH3A2 10A 20 NM_020182 TMEPAI 10A 20 NM_013269 CLEC2D 10A 20 NM_052880 MGC17330 10A 20 NM_003633 ENC1 10A 20 NM_005596 NFIB 10A 20 NM_006874 ELF2 10A 20 NM_014226 RAGE HER2 20 NM_032830 CIRH1A HER2 20 NM_138578 BCL2L1 10A 20 NM_001995 ACSL1 10A 20 NM_001007069 SDCBP 10A 20 NM_152227 SNX5 HER2/E7 20 NM_199329 SLC43A3 10A 20 NM_004053 BYSL 10A 20 NM_013269 CLEC2D HER2 20 NM_002638 PI3 HER2 20 NM_003127 SPTAN1 10A 20 NM_015274 MAN2B2 10A 20 NM_003254 TIMP1 HER2 20 NM_006486 FBLN1 10A 20 NM_016292 TRAP1 10A 20 NM_002178 IGFBP6 HER2/E7 20 NM_002467 MYC HER2/E7 20 NM_002970 SAT1 10A 20 NM_022767 ISG20L1 HER2 20 NM_004864 GDF15 HER2 20 NM_057158 DUSP4 HER2 21 NM_017671 C20orf42 HER2/E7 file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

21 NM_032331 MGC2408 HER2 21 NM_021203 SRPRB HER2 21 NM_002526 NT5E HER2/E7 21 NM_020158 EXOSC5 HER2 21 NM_000666 ACY1 HER2 21 NM_003500 ACOX2 HER2 21 NM_001826 CKS1B HER2 21 NM_001002857 ANXA2 HER2/E7 21 NM_174889 NDUFA12L HER2 21 NM_015440 MTHFD1L HER2 21 NM_031286 SH3BGRL3 HER2/E7 21 NM_001323 CST6 HER2/E7 21 NM_001018 RPS15 HER2/E7 21 NM_002526 NT5E HER2 21 NM_001024666 SH3KBP1 HER2 21 NM_175617 MT1E 10A 21 NM_003793 CTSF 10A 21 NM_000532 PCCB HER2 21 NM_015201 BOP1 HER2 21 NM_001827 CKS2 10A 21 NM_005950 MT1G HER2/E7 21 NM_005978 S100A2 HER2/E7 21 NM_005978 S100A2 HER2 21 NM_181597 UPP1 HER2 21 NM_001011 RPS7 HER2/E7 21 NM_003486 SLC7A5 HER2/E7 21 NM_006042 HS3ST3A1 HER2 22 NM_021034 IFITM3 HER2 22 NM_003806 HRK HER2 22 NM_001307 CLDN7 HER2 22 NM_015374 UNC84B HER2 22 NM_030754 SAA2 HER2 22 NM_002648 PIM1 HER2 22 NM_013974 DDAH2 HER2 22 NM_181782 NCOA7 HER2 22 NM_020376 PNPLA2 HER2 22 NM_004708 PDCD5 10A 22 NM_002970 SAT1 HER2 22 NM_001549 IFIT3 HER2 22 NM_002557 OVGP1 10A 22 NM_002423 MMP7 HER2/E7 22 NM_002053 GBP1 HER2 22 NM_007021 C10orf10 10A 23 NM_016621 PHF21A HER2 23 NM_020247 CABC1 HER2 23 NM_001031806 ALDH3A2 HER2 23 NM_003243 TGFBR3 HER2 23 NM_006876 B3GNT1 HER2 23 NM_003204 NFE2L1 HER2 23 NM_004417 DUSP1 HER2 23 NM_006379 SEMA3C HER2 23 NM_001007069 SDCBP HER2 23 NM_001731 BTG1 HER2 23 NM_001995 ACSL1 HER2

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

23 NM_002578 PAK3 HER2 23 NM_004148 NINJ1 HER2 23 NM_004089 TSC22D3 HER2 23 NM_006079 CITED2 HER2 23 NM_001706 BCL6 HER2 23 NM_003739 AKR1C3 HER2 23 NM_001039 SCNN1G HER2/E7 24 NM_002198 IRF1 HER2 24 NM_020529 NFKBIA HER2 24 NM_181785 LOC283537 HER2 24 NM_022366 TFB2M 10A 24 NM_015274 MAN2B2 HER2 24 NM_004512 IL11RA HER2 24 NM_001008212 OPTN HER2 24 NM_138720 HIST1H2BD HER2/E7 24 NM_004428 EFNA1 HER2 24 NM_020428 SLC44A2 HER2 24 NM_005419 STAT2 HER2 24 NM_005381 NCL 10A 24 NM_006454 MXD4 10A 24 NM_002527 NTF3 HER2/E7 24 NM_006022 TSC22D1 10A 24 NM_000820 GAS6 HER2 24 NM_003516 HIST2H2AA3 10A 24 NM_006290 TNFAIP3 HER2 24 NM_006486 FBLN1 HER2 24 NM_006509 RELB HER2 24 NM_005764 PDZK1IP1 HER2 24 NM_032830 CIRH1A 10A 24 NM_006471 MRCL3 10A 24 NM_004445 EPHB6 10A 24 NM_033405 PRIC285 HER2 24 NM_000422 KRT17 HER2/E7 25 NM_003516 HIST2H2AA3 HER2 25 NM_021626 SCPEP1 HER2 25 NM_145693 LPIN1 10A 25 NM_032812 PLXDC2 10A 25 NM_001312 CRIP2 HER2/E7 25 NM_003877 SOCS2 10A 25 NM_020196 XAB2 10A 25 NM_006328 RBM14 HER2 25 NM_000336 SCNN1B HER2 25 NM_005410 SEPP1 HER2 25 NM_020244 CHPT1 HER2 25 NM_003254 TIMP1 10A 25 NM_000196 HSD11B2 HER2 25 NM_004445 EPHB6 HER2 26 NM_002539 ODC1 HER2 26 NM_005628 SLC1A5 HER2 26 NM_153824 PYCR1 HER2 26 NM_016445 PLEK2 HER2 26 NM_002161 IARS HER2 26 NM_133436 ASNS HER2/E7 26 NM_021154 PSAT1 HER2/E7 file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

26 NM_181353 ID1 HER2 26 NM_139314 ANGPTL4 HER2/E7 26 NM_133436 ASNS HER2 26 NM_004669 CLIC3 10A 26 NM_021154 PSAT1 HER2 26 NM_003914 CCNA1 HER2 27 NM_015444 TMEM158 HER2/E7 27 NM_004990 MARS HER2 27 NM_001794 CDH4 HER2 28 NM_032993 NOLA1 10A 28 NM_015444 TMEM158 10A 28 NM_006033 LIPG 10A 28 NM_000396 CTSK 10A 28 NM_198175 NME1 HER2 28 NM_005950 MT1G HER2 28 NM_017671 C20orf42 HER2 28 NM_001018 RPS15 HER2 28 NM_007208 MRPL3 10A 29 NM_014454 SESN1 HER2 29 NM_018973 DPM3 10A 29 NM_005195 CEBPD HER2 29 NM_004117 FKBP5 HER2 29 NM_024039 MIS12 10A 29 NM_001018109 PIR HER2 29 NM_000990 RPL27A HER2 29 NM_001146 ANGPT1 HER2 29 NM_000076 CDKN1C HER2/E7 29 NM_002964 S100A8 HER2 29 NM_006006 ZBTB16 10A 29 NM_001039 SCNN1G HER2 29 NM_001008540 CXCR4 HER2 29 NM_000691 ALDH3A1 HER2 29 NM_007021 C10orf10 HER2 30 NM_198830 ACLY HER2 30 NM_033405 PRIC285 10A 30 NM_001102 ACTN1 HER2 30 NM_001629 ALOX5AP HER2 30 NM_001010924 C10orf38 HER2 30 NM_003290 TPM4 HER2 30 NM_004603 STX1A 10A 30 NM_004078 CSRP1 HER2 30 NM_002658 PLAU HER2 30 NM_016639 TNFRSF12A HER2 30 NM_003670 BHLHB2 HER2 30 NM_015444 TMEM158 HER2 30 NM_004772 C5orf13 HER2 30 NM_001008212 OPTN 10A 30 NM_003633 ENC1 HER2 31 NM_006079 CITED2 HER2/E7 31 NM_148177 FBXO32 HER2 31 NM_004669 CLIC3 HER2 32 NM_006623 PHGDH HER2 32 NM_001011 RPS7 HER2 32 NM_152227 SNX5 HER2

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] List of All Genes

32 NM_002160 TNC 10A 33 NM_001547 IFIT2 HER2 33 NM_002423 MMP7 HER2 33 NM_012280 FTSJ1 10A 33 NM_148177 FBXO32 HER2/E7 33 NM_005319 HIST1H1C HER2 33 NM_000422 KRT17 HER2 33 NM_000336 SCNN1B HER2/E7

This report was generated by CAGED v1.0.

file:///C|/... analysis of isogenics IPA/2009.11 Differential Analysis IPA/All Isogenics Up & Down/isogenics common CAGED/allgenes.html[11/17/2009 1:43:51 PM] Genes Common to HER2 and HER2/E7, up and down regulated

CAGED Report (November 17, 2009) Genes Common to HER2 and HER2/E7, up and down regulated

Materials

The complete database comprises 16 expression measurements of 424 genes. The recorded expression values range between -3.795817 and 4.530503, with an average expression value of .000.

Methods

The analytical task is to partition the genes into clusters sharing a similar behavior over the 16 different conditions. This cluster analysis was performed using CAGED (1).

We assume the observations to be generated by a polynomial model of order 7, and set the prior precision and the gamma value to 1 and 0, respectively. Polynomial models capture the pattern of dynamics along time. The prior precision is the size of the sample upon which the prior distribution is built, while the gamma value is the rate to zero of the prior precision, with 0 representing the case of perfect ignorance. The method requires a similarity measure to guide the search procedure and a Euclidean distance distance measure between gene profiles was adopted. Note that this measure is used only for search purposes and it is not involved in the actual decision to merge a set of gene profiles together. Goodness of fit of the resulting model is assessed by checking the normality of the standardized residuals of each cluster. Details about this clustering method can be found in (1).

Results

The cluster analysis described in the Methods section yields 13 clusters. Figure 1 draws the expression profiles of the members of each cluster.

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file:///C|/...ifferential analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged.html[11/17/2009 2:37:08 PM] Genes Common to HER2 and HER2/E7, up and down regulated

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Figure 1. Plots of individual gene expression profiles partitioned by cluster membership. Click on the images to enlarge.

Figure 2 shows the dendrogram of the hierarchical structure of the clustering model together with the gene expression profiles (2). The left hand side of the picture shows 13 parallel hierarchies, one for each identified cluster. The order of the clusters follows, from top to bottom, the indexing reported in Table 1. Integers at the branching points of the trees report, on a logarithmic scale, the Bayes factor of each merging. The Bayes factor is the ratio between the posterior probabilities of two models and, in this case, indicates how many times more probable is the clustering model in which the two branches are merged than the clustering model in which they are kept separated. The central part of the drawing displays the expression values of each gene expression profile. Expression values higher or lower than 0 are reported in two different colors. The intensity of each color is proportional to the distance of each value from the cutpoint 0. The last row reports a brief description of each gene in the database.

Figure 3 draws the expression profiles of each of the 13 identified clusters. A cluster profile is the prototypical behavior of its members computed as pointwise average of the gene profiles comprises in the cluster.

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Residuals Index Elements RSS Coefficients Mean SD Skewness Kurtosis .143 -2.836 1.563 - 1 13 114.510 .382 .053 -.004 .000 -.534 4.600 -.623 3.369 -.000 -.250 .110 .039 -.046 2 48 53.313 .011 -.001 .000 - .050 .877 .666 5.219 .000 -1.137 1.195 -.800 3 45 44.271 .243 -.037 .003 -.000 4.036 .929 -.150 2.920 .000 -.436 .260 -.178 .050 4 57 5.121 -.006 .000 -.000 - 3.077 1.974 -.172 2.898 .000 .101 -.270 .187 -.067 5 33 8.505 .012 -.001 .000 - -1.725 1.227 .091 2.640 .000 .479 -.295 .253 -.090 6 33 8.593 .015 -.001 .000 - -1.991 1.801 .197 3.646 .000 .067 -.231 .083 -.002 7 77 62.992 -.002 .000 -.000 .303 1.249 -.118 2.921 .000 .570 .181 -.042 -.002 8 29 35.180 .000 .000 -.000 -.817 1.345 .071 3.037 .000 .673 -.558 .340 -.100 9 27 39.012 .015 -.001 .000 - -2.088 1.754 .207 3.612 .000 .484 -.325 .264 -.083 10 27 23.322 .012 -.001 .000 - -.242 .915 .234 3.027 .000 -.637 .023 -.215 .124 11 31 47.315 -.024 .002 -.000 1.846 2.156 -.010 1.817 .000 -2.086 1.666 -1.074 12 2 6.289 .315 -.046 .003 -.000 3.790 .313 .817 3.945 .000 4.778 -4.494 2.880 - 13 2 4.996 .863 .130 -.010 .000 -2.016 8.000 .158 1.878 -.000

A critical aspect of statistical inference is to assess the goodness of fit of the learned model. In our case, diagnostic analysis of the statistical model is performed by checking the normality of the standardized residuals of each cluster. Cluster residuals are computed by rescaling the differences between the observed values and the values predicted by the model fitted for each cluster. The rescaling factor is the inter-cluster variability. A good fit produces residuals following approximatively a normal distribution with mean 0 and standard deviation 1. The last four columns of Table 1 report the descriptive statistics of the residuals of each cluster. For a sample from a normal distribution, skewness, a measure of asymmetry, should be close to 0 and Kurtosis close to 3. For small clusters , such as cluster 12, 13, containing less than 12 series, deviance from these values may be due to the limited number of available residuals rather than departure from normality. Figure 4 draws the distribution of the residuals for each cluster.

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A complete list of the genes included in the analysis and their cluster assignment is available here.

References

This report was generated by CAGED v1.0.

file:///C|/...ifferential analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged.html[11/17/2009 2:37:08 PM] List of All Genes

CAGED Report (November 17, 2009)

List of All Genes

Cluster Accession Number Description 1 NM_014059 RGC32 HER2 1 NM_003695 LY6D HER2 1 NM_030928 CDT1 HER2 1 NM_133504 DCN HER2 1 NM_000900 MGP HER2 1 NM_002153 HSD17B2 HER2 1 NM_005252 FOS HER2 1 NM_005980 S100P HER2 1 NM_005252 FOS HER2/E7 1 NM_014059 RGC32 HER2/E7 1 NM_003937 KYNU HER2/E7 1 NM_005771 DHRS9 HER2/E7 1 NM_133504 DCN HER2/E7 2 NM_016072 GOLT1B HER2 2 NM_002013 FKBP3 HER2 2 NM_006916 RPE HER2 2 NM_004539 NARS HER2 2 NM_002834 PTPN11 HER2 2 NM_005530 IDH3A HER2 2 NM_003350 UBE2V2 HER2 2 NM_005003 NDUFAB1 HER2 2 NM_012342 BAMBI HER2/E7 2 NM_001003703 ATP5J HER2 2 NM_017929 PEX26 HER2 2 NM_138395 MARS2 HER2/E7 2 NM_005002 NDUFA9 HER2 2 NM_152713 STT3A HER2 2 NM_014399 TSPAN13 HER2 2 NM_002951 RPN2 HER2 2 NM_001970 EIF5A HER2 2 NM_003144 SSR1 HER2 2 NM_018946 NANS HER2 2 NM_006389 HYOU1 HER2 2 NM_007173 PRSS23 HER2 2 NM_005562 LAMC2 HER2 2 NM_005274 GNG5 HER2 2 NM_005449 FAIM3 HER2 2 NM_181876 PPP2R2C HER2 2 NM_001457 FLNB HER2/E7 2 NM_002204 ITGA3 HER2/E7 2 NM_021972 SPHK1 HER2/E7 2 NM_006932 SMTN HER2/E7 2 NM_001018073 PCK2 HER2 2 NM_015599 PGM3 HER2 2 NM_033274 ADAM19 HER2/E7 2 NM_023925 C1QDC1 HER2

file:///C|/...l analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged/allgenes.html[11/17/2009 2:36:55 PM] List of All Genes

2 NM_002204 ITGA3 HER2 2 NM_004730 ETF1 HER2 2 NM_023925 C1QDC1 HER2/E7 2 NM_001859 SLC31A1 HER2 2 NM_001013251 SLC3A2 HER2 2 NM_007080 LSM6 HER2 2 NM_013330 NME7 HER2 2 NM_003975 SH2D2A HER2 2 NM_005851 CDK2AP2 HER2 2 NM_152295 TARS HER2 2 NM_006932 SMTN HER2 2 NM_006096 NDRG1 HER2/E7 2 NM_022842 CDCP1 HER2/E7 2 NM_003975 SH2D2A HER2/E7 2 NM_001797 CDH11 HER2 3 NM_002654 PKM2 HER2/E7 3 NM_016142 HSD17B12 HER2/E7 3 NM_019107 C19orf10 HER2 3 NM_003953 MPZL1 HER2 3 NM_020371 AVEN HER2 3 NM_014060 MCTS1 HER2 3 NM_002237 KCNG1 HER2 3 NM_181671 PITPNC1 HER2 3 NM_021628 ALOXE3 HER2 3 NM_145262 GLYCTK HER2 3 NM_170783 ZNRD1 HER2 3 NM_004324 BAX HER2 3 NM_000178 GSS HER2 3 NM_017933 PID1 HER2 3 NM_016399 TRIAP1 HER2 3 NM_015907 LAP3 HER2 3 NM_013338 ALG5 HER2 3 NM_005005 NDUFB9 HER2 3 NM_000137 FAH HER2 3 NM_178324 SPTLC1 HER2 3 NM_006260 DNAJC3 HER2 3 NM_004093 EFNB2 HER2/E7 3 NM_003299 HSP90B1 HER2 3 NM_016142 HSD17B12 HER2 3 NM_199001 MGC59937 HER2 3 NM_030810 TXNDC5 HER2 3 NM_005980 S100P HER2/E7 3 NM_001159 AOX1 HER2/E7 3 NM_004793 LONP1 HER2 3 NM_005213 CSTA HER2 3 NM_181876 PPP2R2C HER2/E7 3 NM_014216 ITPK1 HER2 3 NM_002654 PKM2 HER2 3 NM_006096 NDRG1 HER2 3 NM_002951 RPN2 HER2/E7 3 NM_003299 HSP90B1 HER2/E7 3 NM_178862 STT3B HER2/E7 3 NM_152713 STT3A HER2/E7 3 NM_000178 GSS HER2/E7 file:///C|/...l analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged/allgenes.html[11/17/2009 2:36:55 PM] List of All Genes

3 NM_014399 TSPAN13 HER2/E7 3 NM_024536 CHPF HER2/E7 3 NM_001150 ANPEP HER2/E7 3 NM_145262 GLYCTK HER2/E7 3 NM_199001 MGC59937 HER2/E7 3 NM_006142 SFN HER2/E7 4 NM_178812 MTDH HER2 4 NM_002056 GFPT1 HER2 4 NM_021628 ALOXE3 HER2/E7 4 NM_003020 SCG5 HER2 4 NM_002503 NFKBIB HER2/E7 4 NM_019107 C19orf10 HER2/E7 4 NM_181671 PITPNC1 HER2/E7 4 NM_152295 TARS HER2/E7 4 NM_013330 NME7 HER2/E7 4 NM_004793 LONP1 HER2/E7 4 NM_201274 M-RIP HER2/E7 4 NM_006795 EHD1 HER2/E7 4 NM_002503 NFKBIB HER2 4 NM_002093 GSK3B HER2/E7 4 NM_033386 MICALL1 HER2/E7 4 NM_000137 FAH HER2/E7 4 NM_202001 ERCC1 HER2 4 NM_005005 NDUFB9 HER2/E7 4 NM_020371 AVEN HER2/E7 4 NM_018946 NANS HER2/E7 4 NM_005002 NDUFA9 HER2/E7 4 NM_003143 SSBP1 HER2/E7 4 NM_001970 EIF5A HER2/E7 4 NM_002834 PTPN11 HER2/E7 4 NM_003144 SSR1 HER2/E7 4 NM_001660 ARF4 HER2/E7 4 NM_030810 TXNDC5 HER2/E7 4 NM_002056 GFPT1 HER2/E7 4 NM_178812 MTDH HER2/E7 4 NM_014060 MCTS1 HER2/E7 4 NM_178324 SPTLC1 HER2/E7 4 NM_012267 HSPBP1 HER2/E7 4 NM_006260 DNAJC3 HER2/E7 4 NM_001018073 PCK2 HER2/E7 4 NM_015599 PGM3 HER2/E7 4 NM_005003 NDUFAB1 HER2/E7 4 NM_003372 VBP1 HER2/E7 4 NM_015907 LAP3 HER2/E7 4 NM_002524 NRAS HER2/E7 4 NM_013338 ALG5 HER2/E7 4 NM_007080 LSM6 HER2/E7 4 NM_016070 MRPS23 HER2/E7 4 NM_202001 ERCC1 HER2/E7 4 NM_005274 GNG5 HER2/E7 4 NM_005213 CSTA HER2/E7 4 NM_080678 UBE2F HER2/E7 4 NM_006389 HYOU1 HER2/E7 4 NM_002013 FKBP3 HER2/E7

file:///C|/...l analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged/allgenes.html[11/17/2009 2:36:55 PM] List of All Genes

4 NM_003953 MPZL1 HER2/E7 4 NM_016070 MRPS23 HER2 4 NM_003143 SSBP1 HER2 4 NM_012267 HSPBP1 HER2 4 NM_003372 VBP1 HER2 4 NM_012328 DNAJB9 HER2 4 NM_002237 KCNG1 HER2/E7 4 NM_005449 FAIM3 HER2/E7 4 NM_004324 BAX HER2/E7 5 NM_016072 GOLT1B HER2/E7 5 NM_139265 EHD4 HER2/E7 5 NM_012479 YWHAG HER2/E7 5 NM_005552 KNS2 HER2/E7 5 NM_080678 UBE2F HER2 5 NM_078483 SLC36A1 HER2/E7 5 NM_004539 NARS HER2/E7 5 NM_001859 SLC31A1 HER2/E7 5 NM_004907 IER2 HER2/E7 5 NM_003350 UBE2V2 HER2/E7 5 NM_182648 BAZ1A HER2/E7 5 NM_183079 PRNP HER2/E7 5 NM_005754 G3BP1 HER2/E7 5 NM_001003703 ATP5J HER2/E7 5 NM_016399 TRIAP1 HER2/E7 5 NM_005530 IDH3A HER2/E7 5 NM_006916 RPE HER2/E7 5 NM_004730 ETF1 HER2/E7 5 NM_003745 SOCS1 HER2/E7 5 NM_017929 PEX26 HER2/E7 5 NM_014216 ITPK1 HER2/E7 5 NM_170783 ZNRD1 HER2/E7 5 NM_002874 RAD23B HER2/E7 5 NM_004309 ARHGDIA HER2/E7 5 NM_018445 SELS HER2/E7 5 NM_005851 CDK2AP2 HER2/E7 5 NM_002874 RAD23B HER2 5 NM_001013251 SLC3A2 HER2/E7 5 NM_020390 EIF5A2 HER2/E7 5 NM_030674 SLC38A1 HER2/E7 5 NM_030674 SLC38A1 HER2 5 NM_004907 IER2 HER2 5 NM_138395 MARS2 HER2 6 NM_001011551 C1GALT1C1 HER2 6 NM_144573 NEXN HER2/E7 6 NM_001386 DPYSL2 HER2 6 NM_005506 SCARB2 HER2 6 NM_018950 HLA-F HER2/E7 6 NM_032520 GNPTG HER2/E7 6 NM_020338 ZMIZ1 HER2/E7 6 NM_004393 DAG1 HER2 6 NM_018462 C3orf10 HER2/E7 6 NM_015329 KIAA0892 HER2/E7 6 NM_015435 RNF19 HER2/E7 6 NM_003695 LY6D HER2/E7 file:///C|/...l analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged/allgenes.html[11/17/2009 2:36:55 PM] List of All Genes

6 NM_001175 ARHGDIB HER2 6 NM_024330 SLC27A3 HER2/E7 6 NM_175859 CTPS2 HER2/E7 6 NM_014183 DYNLRB1 HER2 6 NM_003851 CREG1 HER2/E7 6 NM_001011649 CDK5RAP2 HER2/E7 6 NM_017432 PTOV1 HER2/E7 6 NM_005506 SCARB2 HER2/E7 6 NM_004872 TMEM59 HER2/E7 6 NM_005327 HADH HER2/E7 6 NM_000086 CLN3 HER2/E7 6 NM_014183 DYNLRB1 HER2/E7 6 NM_016118 NUB1 HER2/E7 6 NM_005563 STMN1 HER2/E7 6 NM_018269 ADI1 HER2/E7 6 NM_016118 NUB1 HER2 6 NM_152221 CSNK1E HER2/E7 6 NM_006270 RRAS HER2/E7 6 NM_007308 SNCA HER2/E7 6 NM_001011551 C1GALT1C1 HER2/E7 6 NM_144573 NEXN HER2 7 NM_024330 SLC27A3 HER2 7 NM_004393 DAG1 HER2/E7 7 NM_183239 GSTO2 HER2/E7 7 NM_001466 FZD2 HER2/E7 7 NM_032520 GNPTG HER2 7 NM_015329 KIAA0892 HER2 7 NM_006407 ARL6IP5 HER2 7 NM_018269 ADI1 HER2 7 NM_004935 CDK5 HER2 7 NM_002413 MGST2 HER2 7 NM_018418 SPATA7 HER2 7 NM_001014763 ETFB HER2 7 NM_016245 HSD17B11 HER2 7 NM_003174 SVIL HER2/E7 7 NM_002766 PRPSAP1 HER2/E7 7 NM_000086 CLN3 HER2 7 NM_003730 RNASET2 HER2/E7 7 NM_003761 VAMP8 HER2/E7 7 NM_030971 SFXN3 HER2/E7 7 NM_018418 SPATA7 HER2/E7 7 NM_001752 CAT HER2/E7 7 NM_020300 MGST1 HER2/E7 7 NM_004935 CDK5 HER2/E7 7 NM_002413 MGST2 HER2/E7 7 NM_004872 TMEM59 HER2 7 NM_004528 MGST3 HER2/E7 7 NM_006297 XRCC1 HER2/E7 7 NM_002757 MAP2K5 HER2/E7 7 NM_020533 MCOLN1 HER2/E7 7 NM_006665 HPSE HER2/E7 7 NM_021732 AVPI1 HER2/E7 7 NM_014214 IMPA2 HER2/E7 7 NM_001064 TKT HER2/E7

file:///C|/...l analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged/allgenes.html[11/17/2009 2:36:55 PM] List of All Genes

7 NM_020300 MGST1 HER2 7 NM_006297 XRCC1 HER2 7 NM_000405 GM2A HER2/E7 7 NM_002757 MAP2K5 HER2 7 NM_016219 MAN1B1 HER2 7 NM_030973 MED25 HER2/E7 7 NM_000358 TGFBI HER2/E7 7 NM_002710 PPP1CC HER2/E7 7 NM_006407 ARL6IP5 HER2/E7 7 NM_016219 MAN1B1 HER2/E7 7 NM_001015001 CKMT1A HER2/E7 7 NM_001033604 BBS9 HER2/E7 7 NM_005928 MFGE8 HER2 7 NM_000895 LTA4H HER2 7 NM_004726 REPS2 HER2/E7 7 NM_004062 CDH16 HER2/E7 7 NM_030913 SEMA6C HER2/E7 7 NM_000305 PON2 HER2/E7 7 NM_173354 SNF1LK HER2/E7 7 NM_006287 TFPI HER2/E7 7 NM_016335 PRODH HER2/E7 7 NM_000305 PON2 HER2 7 NM_014553 TFCP2L1 HER2/E7 7 NM_030973 MED25 HER2 7 NM_001033604 BBS9 HER2 7 NM_001333 CTSL2 HER2/E7 7 NM_005375 MYB HER2 7 NM_014214 IMPA2 HER2 7 NM_021105 PLSCR1 HER2 7 NM_003749 IRS2 HER2 7 NM_001860 SLC31A2 HER2/E7 7 NM_007173 PRSS23 HER2/E7 7 NM_005271 GLUD1 HER2/E7 7 NM_002340 LSS HER2/E7 7 NM_005375 MYB HER2/E7 7 NM_000158 GBE1 HER2/E7 7 NM_003749 IRS2 HER2/E7 7 NM_002029 FPR1 HER2/E7 7 NM_002746 MAPK3 HER2/E7 7 NM_021105 PLSCR1 HER2/E7 7 NM_002153 HSD17B2 HER2/E7 7 NM_020338 ZMIZ1 HER2 7 NM_001466 FZD2 HER2 7 NM_000405 GM2A HER2 8 NM_005563 STMN1 HER2 8 NM_018462 C3orf10 HER2 8 NM_007308 SNCA HER2 8 NM_005544 IRS1 HER2/E7 8 NM_001860 SLC31A2 HER2 8 NM_015435 RNF19 HER2 8 NM_173354 SNF1LK HER2 8 NM_004528 MGST3 HER2 8 NM_006456 ST6GALNAC2 HER2 8 NM_001008219 AMY1C HER2/E7 file:///C|/...l analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged/allgenes.html[11/17/2009 2:36:55 PM] List of All Genes

8 NM_001614 ACTG1 HER2/E7 8 NM_006270 RRAS HER2 8 NM_006512 SAA4 HER2 8 NM_006512 SAA4 HER2/E7 8 NM_152221 CSNK1E HER2 8 NM_018950 HLA-F HER2 8 NM_175859 CTPS2 HER2 8 NM_005327 HADH HER2 8 NM_002340 LSS HER2 8 NM_020992 PDLIM1 HER2 8 NM_003637 ITGA10 HER2/E7 8 NM_182648 BAZ1A HER2 8 NM_005544 IRS1 HER2 8 NM_003174 SVIL HER2 8 NM_005803 FLOT1 HER2 8 NM_001008219 AMY1C HER2 8 NM_001614 ACTG1 HER2 8 NM_006435 IFITM2 HER2 8 NM_001012334 MDK HER2 9 NM_201274 M-RIP HER2 9 NM_033386 MICALL1 HER2 9 NM_002524 NRAS HER2 9 NM_024536 CHPF HER2 9 NM_020390 EIF5A2 HER2 9 NM_021972 SPHK1 HER2 9 NM_004309 ARHGDIA HER2 9 NM_005754 G3BP1 HER2 9 NM_018445 SELS HER2 9 NM_183079 PRNP HER2 9 NM_001660 ARF4 HER2 9 NM_001159 AOX1 HER2 9 NM_139265 EHD4 HER2 9 NM_006795 EHD1 HER2 9 NM_022842 CDCP1 HER2 9 NM_004093 EFNB2 HER2 9 NM_012479 YWHAG HER2 9 NM_001150 ANPEP HER2 9 NM_012328 DNAJB9 HER2/E7 9 NM_033274 ADAM19 HER2 9 NM_078483 SLC36A1 HER2 9 NM_005552 KNS2 HER2 9 NM_001457 FLNB HER2 9 NM_001797 CDH11 HER2/E7 9 NM_003745 SOCS1 HER2 9 NM_006142 SFN HER2 9 NM_012342 BAMBI HER2 10 NM_012242 DKK1 HER2 10 NM_005928 MFGE8 HER2/E7 10 NM_002766 PRPSAP1 HER2 10 NM_014315 KLHDC2 HER2 10 NM_003730 RNASET2 HER2 10 NM_030971 SFXN3 HER2 10 NM_017432 PTOV1 HER2 10 NM_001386 DPYSL2 HER2/E7

file:///C|/...l analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged/allgenes.html[11/17/2009 2:36:55 PM] List of All Genes

10 NM_012446 SSBP2 HER2/E7 10 NM_020533 MCOLN1 HER2 10 NM_032409 PINK1 HER2 10 NM_001014763 ETFB HER2/E7 10 NM_003761 VAMP8 HER2 10 NM_000895 LTA4H HER2/E7 10 NM_014315 KLHDC2 HER2/E7 10 NM_030913 SEMA6C HER2 10 NM_020992 PDLIM1 HER2/E7 10 NM_016245 HSD17B11 HER2/E7 10 NM_006435 IFITM2 HER2/E7 10 NM_002275 KRT15 HER2/E7 10 NM_002746 MAPK3 HER2 10 NM_001012334 MDK HER2/E7 10 NM_005803 FLOT1 HER2/E7 10 NM_006456 ST6GALNAC2 HER2/E7 10 NM_030928 CDT1 HER2/E7 10 NM_005384 NFIL3 HER2/E7 10 NM_012242 DKK1 HER2/E7 11 NM_002275 KRT15 HER2 11 NM_014553 TFCP2L1 HER2 11 NM_004726 REPS2 HER2 11 NM_032409 PINK1 HER2/E7 11 NM_016335 PRODH HER2 11 NM_001011649 CDK5RAP2 HER2 11 NM_003637 ITGA10 HER2 11 NM_006086 TUBB3 HER2/E7 11 NM_000358 TGFBI HER2 11 NM_003851 CREG1 HER2 11 NM_006287 TFPI HER2 11 NM_000158 GBE1 HER2 11 NM_001064 TKT HER2 11 NM_002710 PPP1CC HER2 11 NM_005271 GLUD1 HER2 11 NM_021732 AVPI1 HER2 11 NM_005771 DHRS9 HER2 11 NM_003937 KYNU HER2 11 NM_002029 FPR1 HER2 11 NM_004062 CDH16 HER2 11 NM_183239 GSTO2 HER2 11 NM_001175 ARHGDIB HER2/E7 11 NM_001333 CTSL2 HER2 11 NM_178862 STT3B HER2 11 NM_012446 SSBP2 HER2 11 NM_001752 CAT HER2 11 NM_005384 NFIL3 HER2 11 NM_006665 HPSE HER2 11 NM_017933 PID1 HER2/E7 11 NM_001015001 CKMT1A HER2 11 NM_002093 GSK3B HER2 12 NM_005562 LAMC2 HER2/E7 12 NM_003020 SCG5 HER2/E7 13 NM_000900 MGP HER2/E7 13 NM_006086 TUBB3 HER2 file:///C|/...l analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged/allgenes.html[11/17/2009 2:36:55 PM] List of All Genes

This report was generated by CAGED v1.0.

file:///C|/...l analysis of isogenics IPA/2009.11 Differential Analysis IPA/HER2&HER2E7 Up & Down/common to her2 caged/allgenes.html[11/17/2009 2:36:55 PM] MCF10HER2/E7 ONLY UP & DOWN REGULATED

CAGED Report (November 16, 2009) MCF10HER2/E7 ONLY UP & DOWN REGULATED

Materials

The complete database comprises 16 expression measurements of 480 genes. The recorded expression values range between -2.261664 and 4.030066, with an average expression value of -.000.

Methods

The analytical task is to partition the genes into clusters sharing a similar behavior over the 16 different conditions. This cluster analysis was performed using CAGED (1).

Results

The cluster analysis described in the Methods section yields 11 clusters. Figure 1 draws the expression profiles of the members of each cluster.

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Figure 1. Plots of individual gene expression profiles partitioned by cluster membership. Click on the images to enlarge.

Figure 2 shows the dendrogram of the hierarchical structure of the clustering model together with the gene expression profiles (2). The left hand side of the picture shows 11 parallel hierarchies, one for each identified cluster. The order of the clusters follows, from top to bottom, the indexing reported in Table 1. Integers at the branching points of the trees report, on a logarithmic scale, the Bayes factor of each merging. The Bayes factor is the ratio between the posterior probabilities of two models and, in this case, indicates how many times more probable is the clustering model in which the two branches are merged than the clustering model in which they are kept separated. The central part of the drawing displays the expression values of each gene expression profile. Expression values higher or lower than 0 are reported in two different colors. The intensity of each color is proportional to the distance of each value from the cutpoint 0. The last row reports a brief description of each gene in the database.

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Figure 3 draws the expression profiles of each of the 11 identified clusters. A cluster profile is the prototypical behavior of its members computed as pointwise average of the gene profiles comprises in the cluster.

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file:///C|/...lysis IPA/HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC.html[11/16/2009 9:34:21 AM] MCF10HER2/E7 ONLY UP & DOWN REGULATED

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Residuals Index Elements RSS Coefficients Mean SD Skewness Kurtosis -1.226 1.487 -1.120 1 17 14.243 .377 -.063 .005 -.000 4.919 1.199 -.308 2.919 .000 .601 -.517 .416 -.141 2 34 15.004 -2.310 1.815 -.005 2.517 .023 -.002 .000 -.000 .640 -.813 .545 -.164 3 70 18.663 -2.783 1.433 .012 2.849 .025 -.002 .000 -.000 .257 -.413 .209 -.045 4 93 42.881 -.712 1.216 -.030 3.294 .005 -.000 .000 .000 -.603 .538 -.384 .121 5 48 10.290 3.687 1.298 -.066 2.875 -.019 .001 -.000 .000 -.526 .442 -.350 .121 6 37 8.182 3.357 1.525 -.100 2.707 -.020 .002 -.000 .000 -.100 .041 -.041 .010 7 91 33.213 -.001 -.000 .000 -.000 -.161 .905 .054 4.843

.793 -.577 .442 -.149 8 38 26.736 -1.845 1.582 .582 3.307 .024 -.002 .000 -.000 .133 -.653 .216 -.017 9 17 17.650 -.622 2.226 .330 3.233 -.002 .000 -.000 .000 -.300 1.125 -.630 .159 10 21 16.199 -.022 .002 -.000 .000 1.476 1.102 .513 2.942

file:///C|/...lysis IPA/HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC.html[11/16/2009 9:34:21 AM] MCF10HER2/E7 ONLY UP & DOWN REGULATED

-.968 1.316 -.838 .240 11 14 29.105 -.035 .003 -.000 .000 2.367 .732 .239 2.927

A critical aspect of statistical inference is to assess the goodness of fit of the learned model. In our case, diagnostic analysis of the statistical model is performed by checking the normality of the standardized residuals of each cluster. Cluster residuals are computed by rescaling the differences between the observed values and the values predicted by the model fitted for each cluster. The rescaling factor is the inter-cluster variability. A good fit produces residuals following approximatively a normal distribution with mean 0 and standard deviation 1. The last four columns of Table 1 report the descriptive statistics of the residuals of each cluster. For a sample from a normal distribution, skewness, a measure of asymmetry, should be close to 0 and Kurtosis close to 3. For small clusters containing less than 12 series, deviance from these values may be due to the limited number of available residuals rather than departure from normality. Figure 4 draws the distribution of the residuals for each cluster.

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A complete list of the genes included in the analysis and their cluster assignment is available here.

file:///C|/...lysis IPA/HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC.html[11/16/2009 9:34:21 AM] MCF10HER2/E7 ONLY UP & DOWN REGULATED

References

This report was generated by CAGED v1.0.

file:///C|/...lysis IPA/HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC.html[11/16/2009 9:34:21 AM] List of All Genes

CAGED Report (November 16, 2009)

List of All Genes

Cluster Accession Number Description 1 NM_005110 GFPT2 1 NM_002639 SERPINB5 1 NM_001360 DHCR7 1 NM_000527 LDLR 1 NM_198434 AURKA 1 NM_014889 PITRM1 1 NM_016203 PRKAG2 1 NM_007355 HSP90AB1 1 NM_002306 LGALS3 1 NM_002633 PGM1 1 NM_004635 MAPKAPK3 1 NM_152562 CDCA2 1 NM_001889 CRYZ 1 NM_005165 ALDOC 1 NM_004462 FDFT1 1 NM_005860 FSTL3 1 NM_004657 SDPR 2 NM_003920 TIMELESS 2 NM_007370 RFC5 2 NM_024056 TMEM106C 2 NM_006074 TRIM22 2 NM_017651 AHI1 2 NM_020666 CLK4 2 NM_000983 RPL22 2 NM_005778 RBM5 2 NM_032169 ACAD11 2 NM_021145 DMTF1 2 NM_001975 ENO2 2 NM_000022 ADA 2 NM_138300 PYGO2 2 NM_014593 CXXC1 2 NM_003075 SMARCC2 2 NM_020242 KIF15 2 NM_006275 SFRS6 2 NM_004755 RPS6KA5 2 NM_015035 ZHX3 2 NM_007360 KLRK1 2 NM_013409 FST 2 NM_014079 KLF15 2 NM_014755 SERTAD2 2 NM_002975 CLEC11A 2 NM_032844 MASTL 2 NM_203456 PPIE 2 NM_018390 PLCXD1 2 NM_015355 SUZ12 2 NM_004768 SFRS11

file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM] List of All Genes

2 NM_023011 UPF3A 2 NM_005480 TROAP 2 NM_025195 TRIB1 2 NM_001031684 SFRS7 2 NM_021135 RPS6KA2 3 NM_001976 ENO3 3 NM_001002002 GMPR2 3 NM_016243 CYB5R1 3 NM_018453 C14orf11 3 NM_006400 DCTN2 3 NM_020126 SPHK2 3 NM_000181 GUSB 3 NM_147173 NUDT2 3 NM_005176 ATP5G2 3 NM_004773 ZNHIT3 3 NM_000884 IMPDH2 3 NM_006893 LGTN 3 NM_014563 TRAPPC2 3 NM_015917 GSTK1 3 NM_002948 RPL15 3 NM_006570 RRAGA 3 NM_003663 CGGBP1 3 NM_005051 QARS 3 NM_015975 TAF9B 3 NM_003925 MBD4 3 NM_004206 SEC22C 3 NM_001798 CDK2 3 NM_198316 TENC1 3 NM_033389 SSH2 3 NM_001556 IKBKB 3 NM_006231 POLE 3 NM_006301 MAP3K12 3 NM_012423 RPL13A 3 NM_032376 TMEM101 3 NM_002412 MGMT 3 NM_001487 BLOC1S1 3 NM_138443 CCDC5 3 NM_001930 DHPS 3 NM_001033002 RPAIN 3 NM_002925 RGS10 3 NM_007165 SF3A2 3 NM_021173 POLD4 3 NM_173685 NSMCE2 3 NM_006811 SERINC3 3 NM_022092 CHTF18 3 NM_000985 RPL17 3 NM_002931 RING1 3 NM_144998 STRA13 3 NM_005875 EIF1B 3 NM_014380 NGFRAP1 3 NM_020963 MOV10 3 NM_138501 GPSN2 3 NM_032378 EEF1D 3 NM_001675 ATF4 file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM] List of All Genes

3 NM_006044 HDAC6 3 NM_001375 DNASE2 3 NM_004750 CRLF1 3 NM_001005849 SUMO2 3 NM_016441 CRIM1 3 NM_022912 REEP1 3 NM_002905 RDH5 3 NM_007278 GABARAP 3 NM_000946 PRIM1 3 NM_001909 CTSD 3 NM_007246 KLHL2 3 NM_022461 AZI2 3 NM_153813 ZFPM1 3 NM_032451 SPIRE2 3 NM_001733 C1R 3 NM_002444 MSN 3 NM_018467 MDS032 3 NM_006985 NPIP 3 NM_002089 CXCL2 3 NM_001511 CXCL1 3 NM_003542 HIST1H4C 4 NM_016270 KLF2 4 NM_018323 PI4K2B 4 NM_015386 COG4 4 NM_033294 CASP1 4 NM_001662 ARF5 4 NM_032795 RPUSD4 4 NM_178014 TUBB 4 NM_172174 IL15 4 NM_002906 RDX 4 NM_002662 PLD1 4 NM_001359 DECR1 4 NM_130898 CREB3L4 4 NM_006702 PNPLA6 4 NM_000099 CST3 4 NM_001398 ECH1 4 NM_024348 DCTN3 4 NM_032667 BSCL2 4 NM_006111 ACAA2 4 NM_012212 LTB4DH 4 NM_014865 NCAPD2 4 NM_002537 OAZ2 4 NM_003809 TNFSF12 4 NM_001467 SLC37A4 4 NM_016569 TBX3 4 NM_007044 KATNA1 4 NM_014155 ZBTB44 4 NM_013283 MAT2B 4 NM_022087 GALNT11 4 NM_006416 SLC35A1 4 NM_001003786 LYK5 4 NM_002568 PABPC1 4 NM_016448 DTL 4 NM_003472 DEK

file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM] List of All Genes

4 NM_005445 SMC3 4 NM_000318 PXMP3 4 NM_001025616 ARHGAP24 4 NM_000414 HSD17B4 4 NM_033028 BBS4 4 NM_001033 RRM1 4 NM_004674 ASH2L 4 NM_031885 BBS2 4 NM_003390 WEE1 4 NM_031432 UCK1 4 NM_004059 CCBL1 4 NM_007174 CIT 4 NM_018136 ASPM 4 NM_001067 TOP2A 4 NM_004629 FANCG 4 NM_006845 KIF2C 4 NM_001790 CDC25C 4 NM_004701 CCNB2 4 NM_001025778 VRK3 4 NM_022346 NCAPG 4 NM_002655 PLAG1 4 NM_015153 PHF3 4 NM_183359 BRD8 4 NM_152756 RICTOR 4 NM_144608 HEXIM2 4 NM_006339 HMG20B 4 NM_004275 TRFP 4 NM_002439 MSH3 4 NM_001253 CDC5L 4 NM_002501 NFIX 4 NM_031372 HNRPDL 4 NM_015927 TGFB1I1 4 NM_006739 MCM5 4 NM_080737 SYTL4 4 NM_005338 HIP1 4 NM_006410 HTATIP2 4 NM_005290 GPR15 4 NM_001647 APOD 4 NM_005328 HAS2 4 NM_018441 PECR 4 NM_133373 PLCD3 4 NM_033342 TRIM7 4 NM_001628 AKR1B1 4 NM_005178 BCL3 4 NM_002191 INHA 4 NM_001928 CFD 4 NM_003258 TK1 4 NM_000107 DDB2 4 NM_000419 ITGA2B 4 NM_021922 FANCE 4 NM_004723 ARHGEF2 4 NM_018476 BEX1 4 NM_152858 WTAP 4 NM_013238 DNAJC15 file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM] List of All Genes

4 NM_001730 KLF5 4 NM_004456 EZH2 4 NM_006551 SCGB1D2 4 NM_005647 TBL1X 4 NM_004572 PKP2 4 NM_002032 FTH1 5 NM_001032288 UBE2V1 5 NM_003484 HMGA2 5 NM_005648 TCEB1 5 NM_014303 PES1 5 NM_175744 RHOC 5 NM_152653 UBE2E2 5 NM_002865 RAB2A 5 NM_004832 GSTO1 5 NM_006384 CIB1 5 NM_201397 GPX1 5 NM_032731 TXNL5 5 NM_015984 UCHL5 5 NM_183352 SEC13 5 NM_002881 RALB 5 NM_032204 ASCC2 5 NM_020170 NCLN 5 NM_000403 GALE 5 NM_012331 MSRA 5 NM_003149 STAC 5 NM_013336 SEC61A1 5 NM_017510 TMED9 5 NM_005452 WDR46 5 NM_197962 GLRX2 5 NM_013447 EMR2 5 NM_004973 JARID2 5 NM_003059 SLC22A4 5 NM_016167 NOL7 5 NM_024017 HOXB9 5 NM_002634 PHB 5 NM_006809 TOMM34 5 NM_017660 GATAD2A 5 NM_003029 SHC1 5 NM_001084 PLOD3 5 NM_015029 POP1 5 NM_018082 POLR3B 5 NM_015340 LARS2 5 NM_139313 YME1L1 5 NM_018238 AGK 5 NM_005697 SCAMP2 5 NM_004461 FARSA 5 NM_002014 FKBP4 5 NM_014674 EDEM1 5 NM_001819 CHGB 5 NM_001748 CAPN2 5 NM_170587 RGS20 5 NM_001999 FBN2 5 NM_005620 S100A11 5 NM_003234 TFRC

file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM] List of All Genes

6 NM_002786 PSMA1 6 NM_003394 WNT10B 6 NM_003130 SRI 6 NM_033161 SURF4 6 NM_002863 PYGL 6 NM_000754 COMT 6 NM_031427 DNAL1 6 NM_024537 CARS2 6 NM_004599 SREBF2 6 NM_134323 TARBP2 6 NM_005731 ARPC2 6 NM_002809 PSMD3 6 NM_006234 POLR2J 6 NM_006327 TIMM23 6 NM_176795 HRAS 6 NM_001003962 CAPNS1 6 NM_005004 NDUFB8 6 NM_002794 PSMB2 6 NM_001003714 ATP5J2 6 NM_003904 ZNF259 6 NM_024661 CCDC51 6 NM_004763 ITGB1BP1 6 NM_002966 S100A10 6 NM_007008 RTN4 6 NM_005566 LDHA 6 NM_002572 PAFAH1B2 6 NM_006351 TIMM44 6 NM_001188 BAK1 6 NM_006305 ANP32A 6 NM_032515 BOK 6 NM_032375 AKT1S1 6 NM_012138 AATF 6 NM_007267 TMC6 6 NM_023009 MARCKSL1 6 NM_006396 SSSCA1 6 NM_005556 KRT7 6 NM_004343 CALR 7 NM_015196 KIAA0922 7 NM_006753 SURF6 7 NM_181339 IL24 7 NM_004186 SEMA3F 7 NM_001025366 VEGFA 7 NM_015465 GEMIN5 7 NM_005475 SH2B3 7 NM_024769 ASAM 7 NM_002094 GSPT1 7 NM_002355 M6PR 7 NM_004156 PPP2CB 7 NM_007190 SEC23IP 7 NM_005645 TAF13 7 NM_145114 MAX 7 NM_197941 ADAMTS6 7 NM_020162 DHX33 7 NM_002422 MMP3 file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM] List of All Genes

7 NM_005576 LOXL1 7 NM_004953 EIF4G1 7 NM_015658 NOC2L 7 NM_019037 EXOSC4 7 NM_003969 UBE2M 7 NM_145169 SFT2D1 7 NM_004492 GTF2A2 7 NM_015004 EXOSC7 7 NM_006834 RAB32 7 NM_130440 PTPRF 7 NM_004521 KIF5B 7 NM_000641 IL11 7 NM_014056 HIGD1A 7 NM_018227 UBE1L2 7 NM_139078 MAPKAPK5 7 NM_001009913 DKFZp686O24166 7 NM_005109 OXSR1 7 NM_003092 SNRPB2 7 NM_021204 ENOPH1 7 NM_080725 SRXN1 7 NM_078468 BCCIP 7 NM_002748 MAPK6 7 NM_016057 COPZ1 7 NM_001012456 SEC61G 7 NM_170665 ATP2A2 7 NM_016128 COPG 7 NM_007348 ATF6 7 NM_016289 CAB39 7 NM_018290 PGM2 7 NM_005721 ACTR3 7 NM_005324 H3F3B 7 NM_006516 SLC2A1 7 NM_001912 CTSL1 7 NM_004458 ACSL4 7 NM_199327 SPRY1 7 NM_022089 ATP13A2 7 NM_000127 EXT1 7 NM_014604 TAX1BP3 7 NM_201398 FLAD1 7 NM_013376 SERTAD1 7 NM_002370 MAGOH 7 NM_016037 UTP11L 7 NM_021107 MRPS12 7 NM_001239 CCNH 7 NM_001005354 PRR13 7 NM_033109 PNPT1 7 NM_001755 CBFB 7 NM_003885 CDK5R1 7 NM_003155 STC1 7 NM_013370 OSGIN1 7 NM_002928 RGS16 7 NM_017746 TEX10 7 NM_007036 ESM1 7 NM_002859 PXN

file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM] List of All Genes

7 NM_025217 ULBP2 7 NM_144563 RPIA 7 NM_198576 AGRN 7 NM_153339 PUSL1 7 NM_004838 HOMER3 7 NM_013943 CLIC4 7 NM_005311 GRB10 7 NM_018389 SLC35C1 7 NM_001005914 SEMA3B 7 NM_005788 PRMT3 7 NM_012482 ZNF281 7 NM_016645 NGRN 7 NM_133376 ITGB1 7 NM_004733 SLC33A1 7 NM_016038 SBDS 7 NM_003567 BCAR3 7 NM_030980 ISG20L2 7 NM_001010990 HERPUD1 7 NM_006366 CAP2 7 NM_000331 SAA1 8 NM_003611 OFD1 8 NM_012110 CHIC2 8 NM_003820 TNFRSF14 8 NM_006735 HOXA2 8 NM_016056 TMBIM4 8 NM_002129 HMGB2 8 NM_006263 PSME1 8 NM_000234 LIG1 8 NM_005693 NR1H3 8 NM_203488 ACYP1 8 NM_014288 ITGB3BP 8 NM_004453 ETFDH 8 NM_170695 TGIF1 8 NM_021999 ITM2B 8 NM_080546 SLC44A1 8 NM_001182 ALDH7A1 8 NM_001262 CDKN2C 8 NM_001024668 LETMD1 8 NM_030817 APOLD1 8 NM_000991 RPL28 8 NM_005194 CEBPB 8 NM_001698 AUH 8 NM_024629 MLF1IP 8 NM_014871 USP52 8 NM_000050 ASS1 8 NM_001735 C5 8 NM_002261 KLRC3 8 NM_001033506 CSTF3 8 NM_006332 IFI30 8 NM_016286 DCXR 8 NM_001024847 TGFBR2 8 NM_006100 ST3GAL6 8 NM_002676 PMM1 8 NM_203379 ACSL5 file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM] List of All Genes

8 NM_012427 KLK5 8 NM_012244 SLC7A8 8 NM_031300 MXD3 8 NM_018948 ERRFI1 9 NM_152461 ERN1 9 NM_001255 CDC20 9 NM_000700 ANXA1 9 NM_003380 VIM 9 NM_012081 ELL2 9 NM_001799 CDK7 9 NM_005239 ETS2 9 NM_006307 SRPX 9 NM_005733 KIF20A 9 NM_014750 DLG7 9 NM_005225 E2F1 9 NM_004720 EDG4 9 NM_002944 ROS1 9 NM_001964 EGR1 9 NM_001387 DPYSL3 9 NM_002923 RGS2 9 NM_001085 SERPINA3 10 NM_003064 SLPI 10 NM_005168 RND3 10 NM_002546 TNFRSF11B 10 NM_000147 FUCA1 10 NM_003972 BTAF1 10 NM_000376 VDR 10 NM_001613 ACTA2 10 NM_012155 EML2 10 NM_014028 OSTM1 10 NM_003107 SOX4 10 NM_004075 CRY1 10 NM_018993 RIN2 10 NM_003505 FZD1 10 NM_004273 CHST3 10 NM_001003803 ATP5S 10 NM_007279 U2AF2 10 NM_003131 SRF 10 NM_001185 AZGP1 10 NM_000024 ADRB2 10 NM_006931 SLC2A3 10 NM_001554 CYR61 11 NM_001235 SERPINH1 11 NM_006145 DNAJB1 11 NM_001024809 RARA 11 NM_002298 LCP1 11 NM_031207 HYI 11 NM_003840 TNFRSF10D 11 NM_012334 MYO10 11 NM_001539 DNAJA1 11 NM_001005376 PLAUR 11 NM_001878 CRABP2 11 NM_002808 PSMD2 11 NM_005100 AKAP12

file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM] List of All Genes

11 NM_005345 HSPA1A 11 NM_002155 HSPA6

This report was generated by CAGED v1.0.

file:///C|/.../HER2E7 Up & down/2009.11.16 HER2E7 ONLY ALL CAGED MNMC/HER2E7 ONLY UP & DOWN MN MC/allgenes.html[11/16/2009 9:34:45 AM]