Coexpression cluster:C1236: Difference between revisions
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Latest revision as of 11:40, 17 September 2013
Full id: C1236_acute_Mesenchymal_iPS_Skeletal_Bronchial_chronic_embryonic
Phase1 CAGE Peaks
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 |
|---|---|---|---|---|
| 1.01011768964648e-10 | 3.34070889167409e-08 | 4 | 92 | Ribosome (KEGG):03010 |
| 1.05551623749576e-10 | 3.34070889167409e-08 | 4 | 93 | Cytoplasmic Ribosomal Proteins (Wikipathways):WP477 |
| 1.133023502997e-08 | 1.19533979566183e-06 | 4 | 296 | Metabolism of proteins (Reactome):REACT_17015 |
| 2.41231788802606e-10 | 5.08999074373498e-08 | 4 | 114 | Regulation of beta-cell development (Reactome):REACT_13698 |
| 4.66478822294209e-08 | 3.69101368140293e-06 | 4 | 421 | Gene Expression (Reactome):REACT_71 |
| 1.40005596835204e-08 | 1.2660506113812e-06 | 4 | 312 | Diabetes pathways (Reactome):REACT_15380 |
| 6.03784237646204e-10 | 7.64390844860094e-08 | 4 | 143 | Influenza Infection (Reactome):REACT_6167 |
| 5.22856572235584e-10 | 7.64390844860094e-08 | 4 | 138 | {RPS27A,138} (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:0033279 | ribosomal subunit | 8.46541406768146e-08 |
| GO:0005830 | cytosolic ribosome (sensu Eukaryota) | 9.49265585536572e-07 |
| GO:0003735 | structural constituent of ribosome | 4.18593866862922e-06 |
| GO:0005840 | ribosome | 4.45499684263136e-06 |
| GO:0003723 | RNA binding | 5.25917983946982e-06 |
| GO:0044445 | cytosolic part | 5.25917983946982e-06 |
| GO:0030529 | ribonucleoprotein complex | 8.23244723203298e-06 |
| GO:0006412 | translation | 9.11860074703107e-06 |
| GO:0009059 | macromolecule biosynthetic process | 2.28763759932242e-05 |
| GO:0005843 | cytosolic small ribosomal subunit (sensu Eukaryota) | 2.6799510277966e-05 |
| GO:0044249 | cellular biosynthetic process | 4.41598008983352e-05 |
| GO:0005829 | cytosol | 7.04056771737254e-05 |
| GO:0009058 | biosynthetic process | 9.61263843812998e-05 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.000162564217958898 |
| GO:0043228 | non-membrane-bound organelle | 0.000162564217958898 |
| GO:0015934 | large ribosomal subunit | 0.000162564217958898 |
| GO:0015935 | small ribosomal subunit | 0.000203313742897541 |
| GO:0032991 | macromolecular complex | 0.000435587953843731 |
| GO:0044446 | intracellular organelle part | 0.000501752069462546 |
| GO:0044422 | organelle part | 0.000501752069462546 |
| GO:0044444 | cytoplasmic part | 0.000730416704183392 |
| GO:0010467 | gene expression | 0.00138774622843352 |
| GO:0044267 | cellular protein metabolic process | 0.00145860309969479 |
| GO:0044260 | cellular macromolecule metabolic process | 0.00147134878170099 |
| GO:0019538 | protein metabolic process | 0.00162540887295163 |
| GO:0003676 | nucleic acid binding | 0.00219499584095007 |
| GO:0005737 | cytoplasm | 0.00400598022910381 |
| GO:0005842 | cytosolic large ribosomal subunit (sensu Eukaryota) | 0.00753137890643941 |
| GO:0043229 | intracellular organelle | 0.0154713065329693 |
| GO:0043226 | organelle | 0.0154713065329693 |
| GO:0043170 | macromolecule metabolic process | 0.0171758779144423 |
| GO:0005730 | nucleolus | 0.0269440353263539 |
| GO:0044237 | cellular metabolic process | 0.0269440353263539 |
| GO:0044238 | primary metabolic process | 0.026953438245518 |
| GO:0044424 | intracellular part | 0.0278120385522976 |
| GO:0005622 | intracellular | 0.0473496982711292 |
| GO:0043234 | protein complex | 0.0478253109342925 |
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>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| animal cell | 1.29e-39 | 679 |
| eukaryotic cell | 1.29e-39 | 679 |
| embryonic cell | 2.58e-27 | 250 |
| native cell | 1.01e-25 | 722 |
| epithelial cell | 1.07e-19 | 253 |
| somatic cell | 6.65e-18 | 588 |
| electrically responsive cell | 7.82e-14 | 61 |
| electrically active cell | 7.82e-14 | 61 |
| mesodermal cell | 1.74e-13 | 121 |
| muscle precursor cell | 1.81e-13 | 58 |
| myoblast | 1.81e-13 | 58 |
| multi-potent skeletal muscle stem cell | 1.81e-13 | 58 |
| muscle cell | 1.06e-12 | 55 |
| non-terminally differentiated cell | 2.36e-12 | 106 |
| contractile cell | 1.05e-11 | 59 |
| smooth muscle cell | 8.07e-10 | 43 |
| smooth muscle myoblast | 8.07e-10 | 43 |
| squamous epithelial cell | 1.04e-07 | 63 |
| vascular associated smooth muscle cell | 1.11e-07 | 32 |
| endo-epithelial cell | 2.77e-07 | 42 |
| Ontology term | p-value | n |
|---|---|---|
| multilaminar epithelium | 7.15e-14 | 83 |
| unilaminar epithelium | 7.99e-14 | 148 |
| somite | 2.67e-13 | 71 |
| presomitic mesoderm | 2.67e-13 | 71 |
| presumptive segmental plate | 2.67e-13 | 71 |
| dermomyotome | 2.67e-13 | 71 |
| trunk paraxial mesoderm | 2.67e-13 | 71 |
| epithelial vesicle | 3.04e-13 | 78 |
| paraxial mesoderm | 1.03e-12 | 72 |
| presumptive paraxial mesoderm | 1.03e-12 | 72 |
| dense mesenchyme tissue | 1.72e-12 | 73 |
| skeletal muscle tissue | 4.08e-11 | 62 |
| striated muscle tissue | 4.08e-11 | 62 |
| myotome | 4.08e-11 | 62 |
| trunk | 4.86e-10 | 199 |
| muscle tissue | 6.73e-10 | 64 |
| musculature | 6.73e-10 | 64 |
| musculature of body | 6.73e-10 | 64 |
| organism subdivision | 9.42e-10 | 264 |
| trunk mesenchyme | 1.66e-09 | 122 |
| mesenchyme | 6.21e-09 | 160 |
| entire embryonic mesenchyme | 6.21e-09 | 160 |
| vasculature | 1.08e-07 | 78 |
| vascular system | 1.08e-07 | 78 |
| artery | 1.50e-07 | 42 |
| arterial blood vessel | 1.50e-07 | 42 |
| arterial system | 1.50e-07 | 42 |
| epithelial tube open at both ends | 7.10e-07 | 59 |
| blood vessel | 7.10e-07 | 59 |
| blood vasculature | 7.10e-07 | 59 |
| vascular cord | 7.10e-07 | 59 |
| Ontology term | p-value | n |
|---|---|---|
| disease of cellular proliferation | 4.31e-17 | 239 |
| cancer | 3.37e-16 | 235 |
| organ system cancer | 4.40e-08 | 137 |
| cell type cancer | 1.21e-07 | 143 |
| hematologic cancer | 2.51e-07 | 51 |
| immune system cancer | 2.51e-07 | 51 |
| carcinoma | 7.99e-07 | 106 |
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 | 0.0462779 |
| MA0004.1 | 0.502801 |
| MA0006.1 | 0.341337 |
| MA0007.1 | 0.483857 |
| MA0009.1 | 0.973289 |
| MA0014.1 | 0.0156227 |
| MA0017.1 | 0.991615 |
| MA0019.1 | 0.652951 |
| MA0024.1 | 0.867125 |
| MA0025.1 | 1.10816 |
| MA0027.1 | 2.59001 |
| MA0028.1 | 0.35747 |
| MA0029.1 | 0.886702 |
| MA0030.1 | 0.875089 |
| MA0031.1 | 0.809638 |
| MA0038.1 | 0.60704 |
| MA0040.1 | 0.892629 |
| MA0041.1 | 0.521615 |
| MA0042.1 | 0.48922 |
| MA0043.1 | 0.973609 |
| MA0046.1 | 0.962263 |
| MA0048.1 | 0.120314 |
| MA0050.1 | 0.490116 |
| MA0051.1 | 3.64702 |
| MA0052.1 | 0.896548 |
| MA0055.1 | 0.0407081 |
| MA0056.1 | 0 |
| MA0057.1 | 0.115382 |
| MA0058.1 | 0.406232 |
| MA0059.1 | 0.404929 |
| MA0060.1 | 0.224688 |
| MA0061.1 | 0.198335 |
| MA0063.1 | 0 |
| MA0066.1 | 0.607474 |
| MA0067.1 | 1.29359 |
| MA0068.1 | 0.488375 |
| MA0069.1 | 0.958358 |
| MA0070.1 | 0.947018 |
| MA0071.1 | 0.567661 |
| MA0072.1 | 0.942461 |
| MA0073.1 | 0.000265001 |
| MA0074.1 | 0.60198 |
| MA0076.1 | 0.422297 |
| MA0077.1 | 0.934645 |
| MA0078.1 | 0.703614 |
| MA0081.1 | 0.405093 |
| MA0083.1 | 0.980893 |
| MA0084.1 | 1.48179 |
| MA0087.1 | 0.939982 |
| MA0088.1 | 0.252594 |
| MA0089.1 | 0 |
| MA0090.1 | 0.436918 |
| MA0091.1 | 0.505453 |
| MA0092.1 | 0.467172 |
| MA0093.1 | 0.344385 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.621149 |
| MA0101.1 | 0.347695 |
| MA0103.1 | 0.332048 |
| MA0105.1 | 0.104569 |
| MA0106.1 | 0.648997 |
| MA0107.1 | 0.274127 |
| MA0108.2 | 0.806528 |
| MA0109.1 | 0 |
| MA0111.1 | 0.45062 |
| MA0113.1 | 0.665691 |
| MA0114.1 | 0.741402 |
| MA0115.1 | 1.21667 |
| MA0116.1 | 1.39213 |
| MA0117.1 | 1.01134 |
| MA0119.1 | 0.388712 |
| MA0122.1 | 1.03753 |
| MA0124.1 | 1.17486 |
| MA0125.1 | 1.0901 |
| MA0130.1 | 0 |
| MA0131.1 | 0.722072 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.00402 |
| MA0136.1 | 0.614215 |
| MA0139.1 | 0.186511 |
| MA0140.1 | 0.564957 |
| MA0141.1 | 1.04059 |
| MA0142.1 | 0.777365 |
| MA0143.1 | 0.66587 |
| MA0144.1 | 0.708913 |
| MA0145.1 | 0.581146 |
| MA0146.1 | 0.324987 |
| MA0147.1 | 0.281049 |
| MA0148.1 | 0.528066 |
| MA0149.1 | 0.555119 |
| MA0062.2 | 2.39331 |
| MA0035.2 | 0.564239 |
| MA0039.2 | 0.0553061 |
| MA0138.2 | 0.704862 |
| MA0002.2 | 0.213296 |
| MA0137.2 | 0.95459 |
| MA0104.2 | 0.223944 |
| MA0047.2 | 0.636643 |
| MA0112.2 | 0.0758925 |
| MA0065.2 | 0.282161 |
| MA0150.1 | 0.430951 |
| MA0151.1 | 0 |
| MA0152.1 | 0.571637 |
| MA0153.1 | 1.07307 |
| MA0154.1 | 0.102476 |
| MA0155.1 | 0.071478 |
| MA0156.1 | 0.36627 |
| MA0157.1 | 0.749547 |
| MA0158.1 | 0 |
| MA0159.1 | 0.281681 |
| MA0160.1 | 0.543522 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0249953 |
| MA0163.1 | 0.0167306 |
| MA0164.1 | 0.678332 |
| MA0080.2 | 0.911393 |
| MA0018.2 | 0.650405 |
| MA0099.2 | 0.572 |
| MA0079.2 | 0.0015479 |
| MA0102.2 | 1.51913 |
| MA0258.1 | 0.245543 |
| MA0259.1 | 0.289405 |
| 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 |
|---|---|---|---|---|
| BATF#10538 | 3 | 10.4390579109873 | 0.0021372507929898 | 0.0123505967780148 |
| BCL3#602 | 6 | 29.6118024032043 | 4.00448178379027e-09 | 3.2776181270946e-07 |
| BCLAF1#9774 | 5 | 15.4661768643727 | 4.07501217827014e-06 | 0.000129555615490519 |
| BRCA1#672 | 7 | 20.1842306432238 | 7.31084756176234e-10 | 6.92865343469054e-08 |
| CHD2#1106 | 7 | 10.3440228341169 | 7.88338195961115e-08 | 4.72365191325203e-06 |
| CTBP2#1488 | 3 | 26.8787144311406 | 0.000135090303129668 | 0.0017700032829707 |
| E2F4#1874 | 4 | 7.23889160873397 | 0.00111774143052487 | 0.007666368770118 |
| E2F6#1876 | 5 | 3.58368266549813 | 0.00459810189782724 | 0.0217274981498135 |
| ELF1#1997 | 7 | 4.25809795880754 | 3.93848941900192e-05 | 0.000735440544307423 |
| ELK4#2005 | 4 | 9.27753237626744 | 0.000432817858966577 | 0.00404284629036851 |
| EP300#2033 | 6 | 5.80623576533417 | 6.3256174139893e-05 | 0.00103225180796817 |
| ETS1#2113 | 5 | 6.94911494443024 | 0.000201406263333039 | 0.0023935672207828 |
| FAM48A#55578 | 2 | 330.048214285714 | 1.55944547998347e-05 | 0.000365500283850974 |
| FOSL2#2355 | 3 | 7.25580025909787 | 0.00602077509384975 | 0.0269872845504967 |
| FOXA1#3169 | 4 | 6.33223985679169 | 0.00185468101692017 | 0.0109435610579732 |
| GABPB1#2553 | 4 | 4.03867647781838 | 0.0098011349469615 | 0.036850051577713 |
| GATA3#2625 | 3 | 11.6727927245169 | 0.00154910869847361 | 0.00984467344285538 |
| GTF2B#2959 | 7 | 31.9438299343242 | 2.93605109232773e-11 | 3.41467973309149e-09 |
| GTF2F1#2962 | 7 | 12.7396608767577 | 1.83364622006546e-08 | 1.31889929461031e-06 |
| HDAC2#3066 | 4 | 7.66606870664358 | 0.000898637344705782 | 0.00668657634965283 |
| HEY1#23462 | 7 | 4.04011104310571 | 5.68979821988558e-05 | 0.000950626837764566 |
| HNF4A#3172 | 4 | 13.2184516359735 | 0.000109930254651323 | 0.00152855889569025 |
| HNF4G#3174 | 4 | 16.4305271579696 | 4.70133893497423e-05 | 0.000822175380157022 |
| IRF1#3659 | 5 | 5.45511696683136 | 0.0006415794721055 | 0.00525949124703503 |
| IRF3#3661 | 2 | 13.4234149175685 | 0.0088581602305654 | 0.0336169112034891 |
| IRF4#3662 | 4 | 12.5225786781395 | 0.000135673113103555 | 0.00177674786952003 |
| JUNB#3726 | 3 | 13.1188425684948 | 0.0011047899931696 | 0.00767890071187542 |
| JUND#3727 | 6 | 5.99542623588945 | 5.24232039014691e-05 | 0.000891407846347368 |
| KAT2A#2648 | 6 | 528.077142857143 | 1.21570198874926e-16 | 2.44166730774968e-14 |
| MAX#4149 | 7 | 6.45255550900712 | 2.14589603858566e-06 | 7.77098600464106e-05 |
| MEF2A#4205 | 4 | 10.7104176626537 | 0.000248736097009112 | 0.00268282032794946 |
| MEF2C#4208 | 3 | 17.7048662111246 | 0.000461134767071175 | 0.00424807744007642 |
| MYC#4609 | 7 | 5.2222818716094 | 9.4355989882785e-06 | 0.000251004717966586 |
| NANOG#79923 | 5 | 20.8891274864376 | 9.25196150281741e-07 | 3.96986691615755e-05 |
| NFKB1#4790 | 7 | 5.48806342419384 | 6.66568321176054e-06 | 0.000194892858049569 |
| NR2C2#7182 | 5 | 23.2961506466006 | 5.39462754436063e-07 | 2.51185691531645e-05 |
| NR3C1#2908 | 3 | 6.41700999907416 | 0.00849722801565155 | 0.0324333746336756 |
| PAX5#5079 | 6 | 5.71677045529528 | 6.92762487228137e-05 | 0.00109906458155278 |
| POLR2A#5430 | 7 | 2.14745317655807 | 0.00474763644761028 | 0.022346135605569 |
| POU2F2#5452 | 7 | 9.10612405774252 | 1.92426562613847e-07 | 1.0483483449571e-05 |
| REST#5978 | 7 | 9.65002871612802 | 1.28195528172884e-07 | 7.32018193922787e-06 |
| RFX5#5993 | 4 | 6.88452047268291 | 0.00135220703152858 | 0.0089032373071374 |
| RXRA#6256 | 5 | 14.339012242238 | 5.91222266390468e-06 | 0.000177483938716741 |
| SETDB1#9869 | 3 | 17.2800112191473 | 0.00049510103046179 | 0.00437831130570694 |
| SIN3A#25942 | 6 | 4.63618690869869 | 0.000235167814635783 | 0.00256615728688188 |
| SIX5#147912 | 7 | 17.086715355459 | 2.34744782955753e-09 | 2.00134778670334e-07 |
| SMC3#9126 | 3 | 6.44782836211408 | 0.00838431128343785 | 0.0329463874682431 |
| SP1#6667 | 5 | 4.07027241295778 | 0.00254920612899158 | 0.0141119759835552 |
| SP2#6668 | 3 | 11.2086559259334 | 0.00174151533091611 | 0.0107178620887182 |
| SPI1#6688 | 6 | 7.03227729301948 | 2.05436318006376e-05 | 0.000455242173058941 |
| SRF#6722 | 6 | 11.8261527961438 | 9.50741412579311e-07 | 4.0661131199169e-05 |
| STAT1#6772 | 5 | 14.7904196408566 | 5.07663030596835e-06 | 0.000156539177007685 |
| STAT2#6773 | 3 | 27.9701876513317 | 0.00012010576817872 | 0.00162799822489517 |
| TAF1#6872 | 7 | 3.34304628574529 | 0.000214233631962245 | 0.00246657990172031 |
| TAF7#6879 | 7 | 11.4330694049239 | 3.91151708659369e-08 | 2.59045613828001e-06 |
| TBP#6908 | 7 | 3.70677068709639 | 0.000103967209750511 | 0.00145144117352408 |
| TCF12#6938 | 6 | 9.1152556304455 | 4.4461156654571e-06 | 0.000139151295770055 |
| TCF7L2#6934 | 4 | 6.15438660750705 | 0.00206467614813804 | 0.0119729434889166 |
| THAP1#55145 | 3 | 13.4439191155077 | 0.00102904083369238 | 0.00728969650885158 |
| TRIM28#10155 | 3 | 7.96736787654108 | 0.00462234126315646 | 0.0218331463607615 |
| WRNIP1#56897 | 5 | 78.4428316781258 | 1.2872343948194e-09 | 1.16699195278249e-07 |
| YY1#7528 | 7 | 4.91117074985386 | 1.45048003565243e-05 | 0.000345465642972642 |
| ZBTB33#10009 | 5 | 22.6176607357008 | 6.24429259373417e-07 | 2.86155188326899e-05 |
| ZEB1#6935 | 4 | 9.65053258145363 | 0.000371891664568925 | 0.00369869474868241 |
| ZNF143#7702 | 6 | 11.5721799019096 | 1.08146108094101e-06 | 4.50166256805092e-05 |
| ZZZ3#26009 | 4 | 136.80754996299 | 1.04657769083544e-08 | 7.8976537177141e-07 |
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.
