Coexpression cluster:C4236: Difference between revisions
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Latest revision as of 12:41, 17 September 2013
Full id: C4236_retinoblastoma_iPS_small_testicular_HES3GFP_teratocarcinoma_rhabdomyosarcoma
Phase1 CAGE Peaks
| Hg19::chr2:47630255..47630333,+ | p1@MSH2 |
| Hg19::chr2:48010276..48010307,+ | p1@MSH6 |
| Hg19::chr2:48010312..48010328,+ | p2@MSH6 |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 6.20976561239697e-07 | 0.000131026054421576 | 2 | 23 | Mismatch repair (KEGG):03430 |
| 0.000130824789291056 | 0.011830298803034 | 2 | 327 | Pathways in cancer (KEGG):05200 |
| 4.64137026602477e-06 | 0.000587597475678735 | 2 | 62 | Colorectal cancer (KEGG):05210 |
| 1.81874953311705e-06 | 0.000287817113615774 | 2 | 39 | Integrated Cancer pathway (Wikipathways):WP1971 |
| 2.89159085690311e-05 | 0.00305062835403278 | 2 | 154 | Integrated Breast Cancer Pathway (Wikipathways):WP1984 |
| 8.83603012040672e-08 | 5.59320706621745e-05 | 2 | 9 | Mismatch repair (Wikipathways):WP531 |
| 2.94534337346891e-07 | 9.32201177702911e-05 | 2 | 16 | {MLH1,20} (Static Module):NA |
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0032357 | oxidized purine DNA binding | 3.29271505890964e-08 |
| GO:0032356 | oxidized DNA binding | 3.29271505890964e-08 |
| GO:0000400 | four-way junction DNA binding | 3.29271505890964e-08 |
| GO:0032301 | MutSalpha complex | 3.29271505890964e-08 |
| GO:0032143 | single thymine insertion binding | 3.29271505890964e-08 |
| GO:0032139 | dinucleotide insertion or deletion binding | 4.93907258836446e-08 |
| GO:0032134 | mispaired DNA binding | 4.93907258836446e-08 |
| GO:0032137 | guanine/thymine mispair binding | 4.93907258836446e-08 |
| GO:0032142 | single guanine insertion binding | 4.93907258836446e-08 |
| GO:0032300 | mismatch repair complex | 4.93907258836446e-08 |
| GO:0032135 | DNA insertion or deletion binding | 7.59857321286842e-08 |
| GO:0032138 | single base insertion or deletion binding | 7.59857321286842e-08 |
| GO:0000217 | DNA secondary structure binding | 7.59857321286842e-08 |
| GO:0032405 | MutLalpha complex binding | 1.1759696638963e-07 |
| GO:0032404 | mismatch repair complex binding | 3.073200721649e-07 |
| GO:0043531 | ADP binding | 3.70430444127335e-07 |
| GO:0006284 | base-excision repair | 5.76225135309188e-06 |
| GO:0003684 | damaged DNA binding | 1.07562025257715e-05 |
| GO:0030983 | mismatched DNA binding | 2.09260707033337e-05 |
| GO:0006298 | mismatch repair | 2.29392482437372e-05 |
| GO:0045005 | maintenance of fidelity during DNA-dependent DNA replication | 2.29392482437372e-05 |
| GO:0032403 | protein complex binding | 3.77913887443039e-05 |
| GO:0003690 | double-stranded DNA binding | 4.13593643703911e-05 |
| GO:0043566 | structure-specific DNA binding | 8.61662371978417e-05 |
| GO:0006261 | DNA-dependent DNA replication | 8.91008694940949e-05 |
| GO:0006260 | DNA replication | 0.000372850589695633 |
| GO:0032302 | MutSbeta complex | 0.000372850589695633 |
| GO:0000701 | purine-specific mismatch base pair DNA N-glycosylase activity | 0.000372850589695633 |
| GO:0043570 | maintenance of DNA repeat elements | 0.000372850589695633 |
| GO:0032181 | dinucleotide repeat insertion binding | 0.000372850589695633 |
| GO:0006281 | DNA repair | 0.000407000824604192 |
| GO:0000287 | magnesium ion binding | 0.000493471458313944 |
| GO:0006974 | response to DNA damage stimulus | 0.000493471458313944 |
| GO:0000700 | mismatch base pair DNA N-glycosylase activity | 0.000493471458313944 |
| GO:0009719 | response to endogenous stimulus | 0.000656924877524407 |
| GO:0016887 | ATPase activity | 0.000903237472812511 |
| GO:0006301 | postreplication repair | 0.00105801164303689 |
| GO:0017111 | nucleoside-triphosphatase activity | 0.00216842616708457 |
| GO:0016462 | pyrophosphatase activity | 0.00224103793111858 |
| GO:0016818 | hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides | 0.00224103793111858 |
| GO:0016817 | hydrolase activity, acting on acid anhydrides | 0.00224103793111858 |
| GO:0019104 | DNA N-glycosylase activity | 0.00234808105336975 |
| GO:0044428 | nuclear part | 0.00234808105336975 |
| GO:0006950 | response to stress | 0.00279144035012888 |
| GO:0006259 | DNA metabolic process | 0.00285140343528084 |
| GO:0016799 | hydrolase activity, hydrolyzing N-glycosyl compounds | 0.00291701627068806 |
| GO:0003697 | single-stranded DNA binding | 0.00725238356455489 |
| GO:0008022 | protein C-terminus binding | 0.00861303260242305 |
| GO:0005524 | ATP binding | 0.0130414729973987 |
| GO:0032559 | adenyl ribonucleotide binding | 0.0130414729973987 |
| GO:0043234 | protein complex | 0.0134110444302739 |
| GO:0030554 | adenyl nucleotide binding | 0.0136319828171337 |
| GO:0042803 | protein homodimerization activity | 0.0166344703124406 |
| GO:0003677 | DNA binding | 0.0181049202533107 |
| GO:0032553 | ribonucleotide binding | 0.0181049202533107 |
| GO:0032555 | purine ribonucleotide binding | 0.0181049202533107 |
| GO:0017076 | purine nucleotide binding | 0.0191399749681331 |
| GO:0016798 | hydrolase activity, acting on glycosyl bonds | 0.020879621687379 |
| GO:0032991 | macromolecular complex | 0.020879621687379 |
| GO:0045786 | negative regulation of progression through cell cycle | 0.020879621687379 |
| GO:0016787 | hydrolase activity | 0.020879621687379 |
| GO:0044446 | intracellular organelle part | 0.0222817113393344 |
| GO:0044422 | organelle part | 0.0222817113393344 |
| GO:0000166 | nucleotide binding | 0.0233801187807446 |
| GO:0000074 | regulation of progression through cell cycle | 0.029940926774321 |
| GO:0051726 | regulation of cell cycle | 0.029940926774321 |
| GO:0042802 | identical protein binding | 0.029940926774321 |
| GO:0046983 | protein dimerization activity | 0.029940926774321 |
| GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0407929887479537 |
| GO:0051276 | chromosome organization and biogenesis | 0.0424879627039622 |
| GO:0005634 | nucleus | 0.0425424652209084 |
| GO:0003676 | nucleic acid binding | 0.0464864505909484 |
| GO:0022402 | cell cycle process | 0.047444133633493 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br><br>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| neural cell | 3.80e-07 | 25 |
| Ontology term | p-value | n |
|---|---|---|
| cancer | 7.96e-54 | 235 |
| disease of cellular proliferation | 4.16e-52 | 239 |
| cell type cancer | 5.96e-34 | 143 |
| carcinoma | 7.60e-28 | 106 |
| organ system cancer | 3.31e-24 | 137 |
| hematologic cancer | 2.78e-12 | 51 |
| immune system cancer | 2.78e-12 | 51 |
| leukemia | 2.51e-10 | 39 |
| myeloid leukemia | 9.06e-10 | 31 |
| germ cell and embryonal cancer | 1.27e-07 | 22 |
| germ cell cancer | 1.27e-07 | 22 |
| disease of anatomical entity | 2.31e-07 | 39 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 3.8806 |
| MA0004.1 | 0.826076 |
| MA0006.1 | 0.639288 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 2.44638 |
| MA0017.1 | 0.686276 |
| MA0019.1 | 0.990656 |
| MA0024.1 | 2.72668 |
| MA0025.1 | 1.46617 |
| MA0027.1 | 2.95767 |
| MA0028.1 | 0.658629 |
| MA0029.1 | 1.23771 |
| MA0030.1 | 1.22561 |
| MA0031.1 | 1.15713 |
| MA0038.1 | 0.94098 |
| MA0040.1 | 1.24388 |
| MA0041.1 | 0.847069 |
| MA0042.1 | 0.810843 |
| MA0043.1 | 1.32783 |
| MA0046.1 | 1.31611 |
| MA0048.1 | 0.341392 |
| MA0050.1 | 0.81185 |
| MA0051.1 | 0.936307 |
| MA0052.1 | 1.24796 |
| MA0055.1 | 2.37507 |
| MA0056.1 | 0 |
| MA0057.1 | 0.333427 |
| MA0058.1 | 0.716037 |
| MA0059.1 | 0.714521 |
| MA0060.1 | 3.15662 |
| MA0061.1 | 0.456531 |
| MA0063.1 | 0 |
| MA0066.1 | 0.941452 |
| MA0067.1 | 1.65513 |
| MA0068.1 | 0.405474 |
| MA0069.1 | 1.31207 |
| MA0070.1 | 1.30033 |
| MA0071.1 | 0.897953 |
| MA0072.1 | 1.29561 |
| MA0073.1 | 0.211629 |
| MA0074.1 | 0.935474 |
| MA0076.1 | 0.734647 |
| MA0077.1 | 1.28751 |
| MA0078.1 | 1.04495 |
| MA0081.1 | 0.714712 |
| MA0083.1 | 1.33535 |
| MA0084.1 | 1.84562 |
| MA0087.1 | 1.29304 |
| MA0088.1 | 0.715722 |
| MA0089.1 | 0 |
| MA0090.1 | 0.751469 |
| MA0091.1 | 0.829044 |
| MA0092.1 | 0.785956 |
| MA0093.1 | 0.642957 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.956299 |
| MA0101.1 | 0.646932 |
| MA0103.1 | 0.628063 |
| MA0105.1 | 0.31555 |
| MA0106.1 | 0.986396 |
| MA0107.1 | 0.556367 |
| MA0108.2 | 1.15387 |
| MA0109.1 | 0 |
| MA0111.1 | 0.767139 |
| MA0113.1 | 2.29491 |
| MA0114.1 | 0.549955 |
| MA0115.1 | 1.57693 |
| MA0116.1 | 0.560723 |
| MA0117.1 | 1.36676 |
| MA0119.1 | 0.695578 |
| MA0122.1 | 1.39371 |
| MA0124.1 | 1.53432 |
| MA0125.1 | 1.44766 |
| MA0130.1 | 0 |
| MA0131.1 | 1.06461 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.35921 |
| MA0136.1 | 0.948776 |
| MA0139.1 | 1.12079 |
| MA0140.1 | 0.894983 |
| MA0141.1 | 0.712476 |
| MA0142.1 | 1.12317 |
| MA0143.1 | 1.00455 |
| MA0144.1 | 0.531867 |
| MA0145.1 | 0.752137 |
| MA0146.1 | 1.16674 |
| MA0147.1 | 0.565108 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 0.449458 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 4.75888 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 0.476938 |
| MA0137.2 | 0.666381 |
| MA0104.2 | 1.2307 |
| MA0047.2 | 0.973066 |
| MA0112.2 | 0.731309 |
| MA0065.2 | 0.277623 |
| MA0150.1 | 0.744617 |
| MA0151.1 | 0 |
| MA0152.1 | 0.902317 |
| MA0153.1 | 1.43021 |
| MA0154.1 | 0.312019 |
| MA0155.1 | 0.256269 |
| MA0156.1 | 0.669101 |
| MA0157.1 | 1.09377 |
| MA0158.1 | 0 |
| MA0159.1 | 0.565904 |
| MA0160.1 | 0.871361 |
| MA0161.1 | 0 |
| MA0162.1 | 3.52399 |
| MA0163.1 | 0.387745 |
| MA0164.1 | 1.01792 |
| MA0080.2 | 0.643061 |
| MA0018.2 | 0.987913 |
| MA0099.2 | 0.902716 |
| MA0079.2 | 2.28794 |
| MA0102.2 | 1.88331 |
| MA0258.1 | 0.519674 |
| MA0259.1 | 1.40979 |
| MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| E2F1#1869 | 3 | 4.90738921487932 | 0.00846098534723939 | 0.0326373720657557 |
| E2F4#1874 | 3 | 12.6680603152844 | 0.000491798700629898 | 0.00437914268011646 |
| E2F6#1876 | 3 | 5.01715573169739 | 0.0079176980688633 | 0.032320362267501 |
| EGR1#1958 | 3 | 4.98817909481014 | 0.00805648813738344 | 0.0321517602055861 |
| ELF1#1997 | 3 | 4.25809795880754 | 0.0129517987505461 | 0.046360931888415 |
| GABPB1#2553 | 3 | 7.06768383618217 | 0.00283221282541742 | 0.0154485546181527 |
| IRF1#3659 | 3 | 7.6371637535639 | 0.00224469274729724 | 0.0128414475150623 |
| MYC#4609 | 3 | 5.2222818716094 | 0.00702084375574015 | 0.0295284270701412 |
| NRF1#4899 | 3 | 12.2102794477109 | 0.000549217240102001 | 0.0047221288663055 |
| SIN3A#25942 | 3 | 5.40888472681514 | 0.00631896197799152 | 0.0277556491575664 |
| SMARCB1#6598 | 2 | 12.1684771874383 | 0.00867500222192174 | 0.0329997653270911 |
| SP1#6667 | 3 | 5.6983813781409 | 0.00540396270171217 | 0.0247157635473666 |
| TFAP2A#7020 | 2 | 11.0124229153633 | 0.0105499065521556 | 0.0390260223993406 |
| ZBTB7A#51341 | 3 | 7.3519093078759 | 0.00251625586028227 | 0.0140547248792395 |
| ZNF263#10127 | 3 | 8.22184163701068 | 0.00179904392556587 | 0.0109684967041549 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.
