Coexpression cluster:C3237: Difference between revisions
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Latest revision as of 12:22, 17 September 2013
Full id: C3237_Alveolar_Keratocytes_Bronchial_Hepatic_Adipocyte_Mammary_Mesenchymal
Phase1 CAGE Peaks
| Hg19::chr12:110011288..110011347,- | p1@MMAB |
| Hg19::chr12:110011571..110011644,+ | p1@MVK |
| Hg19::chr16:88729473..88729561,- | p1@MVD |
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 |
|---|---|---|---|---|
| 7.72917887211087e-07 | 0.000244628511302309 | 2 | 15 | Terpenoid backbone biosynthesis (KEGG):00900 |
| 6.31961929821581e-05 | 0.0133343967192354 | 3 | 1138 | Metabolic pathways (KEGG):01100 |
| 7.72917887211087e-07 | 0.000244628511302309 | 2 | 15 | Cholesterol Biosynthesis (Wikipathways):WP1795 |
| 0.00030437946951327 | 0.048168051050475 | 2 | 289 | Metabolism of lipids and lipoproteins (Reactome):REACT_22258 |
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:0006695 | cholesterol biosynthetic process | 7.09273028841617e-05 |
| GO:0016126 | sterol biosynthetic process | 7.09273028841617e-05 |
| GO:0008299 | isoprenoid biosynthetic process | 7.09273028841617e-05 |
| GO:0006720 | isoprenoid metabolic process | 9.38540934350304e-05 |
| GO:0008203 | cholesterol metabolic process | 0.000227604976015694 |
| GO:0006694 | steroid biosynthetic process | 0.000236560699903554 |
| GO:0016125 | sterol metabolic process | 0.000236560699903554 |
| GO:0008202 | steroid metabolic process | 0.00116921618164445 |
| GO:0009235 | cobalamin metabolic process | 0.00173694229634674 |
| GO:0009236 | cobalamin biosynthetic process | 0.00173694229634674 |
| GO:0008817 | cob(I)yrinic acid a,c-diamide adenosyltransferase activity | 0.00173694229634674 |
| GO:0008610 | lipid biosynthetic process | 0.00173694229634674 |
| GO:0004163 | diphosphomevalonate decarboxylase activity | 0.00183231096230755 |
| GO:0004496 | mevalonate kinase activity | 0.00183231096230755 |
| GO:0009058 | biosynthetic process | 0.00183231096230755 |
| GO:0006066 | alcohol metabolic process | 0.00230514148065186 |
| GO:0005524 | ATP binding | 0.00230514148065186 |
| GO:0032559 | adenyl ribonucleotide binding | 0.00230514148065186 |
| GO:0030554 | adenyl nucleotide binding | 0.00247528120164151 |
| GO:0016740 | transferase activity | 0.00324351844010408 |
| GO:0032553 | ribonucleotide binding | 0.00365700248173288 |
| GO:0032555 | purine ribonucleotide binding | 0.00365700248173288 |
| GO:0017076 | purine nucleotide binding | 0.00390457841089428 |
| GO:0044255 | cellular lipid metabolic process | 0.00458755989077455 |
| GO:0000166 | nucleotide binding | 0.00577037226642438 |
| GO:0006779 | porphyrin biosynthetic process | 0.00616669659674457 |
| GO:0006629 | lipid metabolic process | 0.00616669659674457 |
| GO:0033014 | tetrapyrrole biosynthetic process | 0.0066630865719394 |
| GO:0006778 | porphyrin metabolic process | 0.0066630865719394 |
| GO:0033013 | tetrapyrrole metabolic process | 0.00727100775665974 |
| GO:0042364 | water-soluble vitamin biosynthetic process | 0.00727100775665974 |
| GO:0009110 | vitamin biosynthetic process | 0.00764686651571054 |
| GO:0016310 | phosphorylation | 0.0106005592510717 |
| GO:0016831 | carboxy-lyase activity | 0.0106005592510717 |
| GO:0006767 | water-soluble vitamin metabolic process | 0.0117660113535449 |
| GO:0016830 | carbon-carbon lyase activity | 0.0133441943385484 |
| GO:0016301 | kinase activity | 0.0133441943385484 |
| GO:0006793 | phosphorus metabolic process | 0.0133441943385484 |
| GO:0006796 | phosphate metabolic process | 0.0133441943385484 |
| GO:0016765 | transferase activity, transferring alkyl or aryl (other than methyl) groups | 0.0133441943385484 |
| GO:0006766 | vitamin metabolic process | 0.0134880903701458 |
| GO:0042579 | microbody | 0.0149481784519316 |
| GO:0005777 | peroxisome | 0.0149481784519316 |
| GO:0016772 | transferase activity, transferring phosphorus-containing groups | 0.0159393085126707 |
| GO:0046483 | heterocycle metabolic process | 0.0185525498427985 |
| GO:0051188 | cofactor biosynthetic process | 0.0306326844695493 |
| GO:0016829 | lyase activity | 0.0378202022513722 |
| GO:0051186 | cofactor metabolic process | 0.0456033012209741 |
| GO:0042802 | identical protein binding | 0.0473782813292496 |
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>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| embryonic cell | 5.46e-10 | 250 |
| epithelial cell | 1.06e-08 | 253 |
| epithelial cell of nephron | 5.83e-07 | 15 |
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 | 1.0927 |
| MA0004.1 | 0.826076 |
| MA0006.1 | 0.639288 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 0.118426 |
| MA0017.1 | 0.686276 |
| MA0019.1 | 2.26702 |
| MA0024.1 | 1.21731 |
| 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 | 2.16573 |
| 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 | 1.90116 |
| MA0051.1 | 0.936307 |
| MA0052.1 | 1.24796 |
| MA0055.1 | 0.190716 |
| MA0056.1 | 0 |
| MA0057.1 | 0.333427 |
| MA0058.1 | 0.716037 |
| MA0059.1 | 0.714521 |
| MA0060.1 | 5.46492 |
| MA0061.1 | 1.15625 |
| 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 | 0.0834661 |
| 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 | 1.55947 |
| MA0103.1 | 0.628063 |
| MA0105.1 | 0.846801 |
| MA0106.1 | 0.986396 |
| MA0107.1 | 1.36919 |
| MA0108.2 | 1.15387 |
| MA0109.1 | 0 |
| MA0111.1 | 0.767139 |
| MA0113.1 | 1.00436 |
| MA0114.1 | 0.549955 |
| MA0115.1 | 1.57693 |
| MA0116.1 | 1.3784 |
| 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 | 0.440097 |
| 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 | 3.00132 |
| MA0147.1 | 0.565108 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 0.449458 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 0.757898 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 0.476938 |
| MA0137.2 | 0.666381 |
| MA0104.2 | 0.491226 |
| MA0047.2 | 0.973066 |
| MA0112.2 | 0.264678 |
| MA0065.2 | 0.277623 |
| MA0150.1 | 0.744617 |
| MA0151.1 | 0 |
| MA0152.1 | 0.902317 |
| MA0153.1 | 1.43021 |
| MA0154.1 | 2.30945 |
| 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 | 0.149099 |
| MA0163.1 | 0.122425 |
| MA0164.1 | 1.01792 |
| MA0080.2 | 0.643061 |
| MA0018.2 | 0.987913 |
| MA0099.2 | 0.902716 |
| MA0079.2 | 0.311277 |
| MA0102.2 | 1.88331 |
| MA0258.1 | 0.519674 |
| MA0259.1 | 0.575594 |
| 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 |
|---|---|---|---|---|
| CCNT2#905 | 3 | 6.33620157696263 | 0.00393075003576489 | 0.0189329706675852 |
| CHD2#1106 | 3 | 10.3440228341169 | 0.000903370110274688 | 0.00658802255058852 |
| E2F1#1869 | 3 | 4.90738921487932 | 0.00846098534723939 | 0.0323933006591273 |
| E2F4#1874 | 3 | 12.6680603152844 | 0.000491798700629898 | 0.00435944359999032 |
| E2F6#1876 | 3 | 5.01715573169739 | 0.0079176980688633 | 0.0320734027078587 |
| ETS1#2113 | 3 | 9.72876092220234 | 0.00108584009258484 | 0.00760488555723362 |
| FOS#2353 | 3 | 8.9979553088944 | 0.00137249927241713 | 0.00895274820510727 |
| FOSL2#2355 | 3 | 16.9302006045617 | 0.000206016205317162 | 0.00242462547522189 |
| HMGN3#9324 | 3 | 8.17854772335059 | 0.00182776694216421 | 0.0108404879137196 |
| IRF1#3659 | 3 | 7.6371637535639 | 0.00224469274729724 | 0.0127714897491271 |
| IRF3#3661 | 3 | 46.9819522114896 | 9.63568551583244e-06 | 0.000253231343630605 |
| MYC#4609 | 3 | 5.2222818716094 | 0.00702084375574015 | 0.0293417327333232 |
| NANOG#79923 | 3 | 29.2447784810127 | 3.99627955670032e-05 | 0.000734543190113033 |
| NFYA#4800 | 3 | 18.4255806998305 | 0.000159813550781416 | 0.00199102557915548 |
| NFYB#4801 | 3 | 16.7597932535365 | 0.000212364992329618 | 0.00245073894297381 |
| PBX3#5090 | 2 | 14.6096751244961 | 0.00605612247321789 | 0.0268120125044681 |
| POU2F2#5452 | 3 | 9.10612405774252 | 0.00132416519268213 | 0.0088001583556175 |
| RFX5#5993 | 3 | 12.0479108271951 | 0.000571724605031258 | 0.00483328039702603 |
| SIN3A#25942 | 3 | 5.40888472681514 | 0.00631896197799152 | 0.0275678211295149 |
| SP1#6667 | 3 | 5.6983813781409 | 0.00540396270171217 | 0.0245630178267014 |
| SP2#6668 | 3 | 26.1535304938446 | 5.58768218891694e-05 | 0.000938067738511969 |
| SREBF1#6720 | 3 | 47.0058494404883 | 9.62099323994382e-06 | 0.000254188442445356 |
| SREBF2#6721 | 3 | 436.943262411348 | 1.19027063774682e-08 | 8.89840194242237e-07 |
| TCF7L2#6934 | 3 | 10.7701765631373 | 0.000800318129839838 | 0.00612115892803683 |
| TFAP2C#7022 | 3 | 10.8092286098602 | 0.000791674657575313 | 0.00613502334069215 |
| YY1#7528 | 3 | 4.91117074985386 | 0.00844145534180826 | 0.0328190133061502 |
| ZEB1#6935 | 2 | 11.2589546783626 | 0.0101022267664633 | 0.0377997442412818 |
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.
