Coexpression cluster:C3953: Difference between revisions
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{{Coexpression_clusters | 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large ribosomal subunit (sensu Eukaryota)!8.11246671004954e-08!6165;6160;6135$GO:0005830!cytosolic ribosome (sensu Eukaryota)!2.99701452344948e-07!6165;6160;6135$GO:0015934!large ribosomal subunit!5.54678852341937e-07!6165;6160;6135$GO:0044445!cytosolic part!2.49698689484997e-06!6165;6160;6135$GO:0033279!ribosomal subunit!3.28124645425421e-06!6165;6160;6135$GO:0005829!cytosol!4.4946882578473e-05!6165;6160;6135$GO:0003735!structural constituent of ribosome!9.91441963952388e-05!6165;6160;6135$GO:0005840!ribosome!0.000112771658049979!6165;6160;6135$GO:0003723!RNA binding!0.000152830307734731!6165;6160;6135$GO:0030529!ribonucleoprotein complex!0.000217462340567173!6165;6160;6135$GO:0006412!translation!0.000235913035980226!6165;6160;6135$GO:0009059!macromolecule biosynthetic process!0.000470758868352947!6165;6160;6135$GO:0044249!cellular biosynthetic process!0.000827081666316246!6165;6160;6135$GO:0009058!biosynthetic process!0.00155979504619136!6165;6160;6135$GO:0043232!intracellular non-membrane-bound organelle!0.00229977448464354!6165;6160;6135$GO:0043228!non-membrane-bound organelle!0.00229977448464354!6165;6160;6135$GO:0032991!macromolecular complex!0.00509120568496683!6165;6160;6135$GO:0044446!intracellular organelle part!0.00548130567723766!6165;6160;6135$GO:0044422!organelle part!0.00548130567723766!6165;6160;6135$GO:0000049!tRNA binding!0.00588633108744147!6165$GO:0044444!cytoplasmic part!0.00681719258441986!6165;6160;6135$GO:0019843!rRNA binding!0.00837260151835178!6135$GO:0010467!gene expression!0.0104299359727179!6165;6160;6135$GO:0044267!cellular protein metabolic process!0.0107018979530247!6165;6160;6135$GO:0044260!cellular macromolecule metabolic process!0.0107018979530247!6165;6160;6135$GO:0019538!protein metabolic process!0.0114328712142776!6165;6160;6135$GO:0003676!nucleic acid binding!0.0142031328827836!6165;6160;6135$GO:0005737!cytoplasm!0.0221219764203332!6165;6160;6135$GO:0005730!nucleolus!0.0290011854976768!6135$GO:0005515!protein binding!0.0357886869663508!6165;6160;6135$GO:0006605!protein targeting!0.0357886869663508!6135|id=C3953|ontology_enrichment_celltype=CL:0000003!4.19e-19!722;CL:0000548!9.05e-15!679;CL:0000255!9.05e-15!679;CL:0002032!2.75e-11!161;CL:0000837!2.75e-11!161;CL:0000860!2.85e-11!42;CL:0002057!2.85e-11!42;CL:0000988!6.29e-11!177;CL:0000037!8.07e-11!168;CL:0000566!8.07e-11!168;CL:0000034!1.92e-10!441;CL:0002031!4.07e-10!120;CL:0002087!4.40e-10!115;CL:0000048!1.80e-09!427;CL:0000723!8.06e-09!433;CL:0002371!1.48e-08!588;CL:0002320!1.58e-08!361;CL:0000473!1.71e-08!48;CL:0000234!1.71e-08!48;CL:0000134!9.03e-08!354;CL:0002242!2.87e-07!55;CL:0000738!6.30e-07!136;CL:0000838!6.54e-07!52;CL:0000542!6.77e-07!53;CL:0000051!6.77e-07!53|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002384!2.52e-08!371|pathway_enrichment=3.23952687815502e-08;1.05948726550059e-05;3;92;Ribosome (KEGG):03010!3.34751110742684e-08;1.05948726550059e-05;3;93;Cytoplasmic Ribosomal Proteins (Wikipathways):WP477!1.1037505066909e-06;0.00011644567845589;3;296;Metabolism of proteins (Reactome):REACT_17015!6.2031341872007e-08;1.30886131349935e-05;3;114;Regulation of beta-cell development (Reactome):REACT_13698!3.18533613032144e-06;0.000252039721311684;3;421;Gene Expression (Reactome):REACT_71!1.29326205516739e-06;0.000116947840131565;3;312;Diabetes pathways (Reactome):REACT_15380!1.23098667822397e-07;1.55842913463155e-05;3;143;Influenza Infection (Reactome):REACT_6167!1.10547371417187e-07;1.55842913463155e-05;3;138;{RPS27A,138} (Static 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Latest revision as of 12:36, 17 September 2013
Full id: C3953_Smooth_CD4_Hair_acute_iPS_xeroderma_Nucleus
Phase1 CAGE Peaks
| Hg19::chr1:24018278..24018303,+ | p1@RPL11 |
| Hg19::chr2:101618729..101618761,+ | p1@RPL31 |
| Hg19::chr3:197677047..197677074,+ | p1@RPL35A |
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 |
|---|---|---|---|---|
| 3.23952687815502e-08 | 1.05948726550059e-05 | 3 | 92 | Ribosome (KEGG):03010 |
| 3.34751110742684e-08 | 1.05948726550059e-05 | 3 | 93 | Cytoplasmic Ribosomal Proteins (Wikipathways):WP477 |
| 1.1037505066909e-06 | 0.00011644567845589 | 3 | 296 | Metabolism of proteins (Reactome):REACT_17015 |
| 6.2031341872007e-08 | 1.30886131349935e-05 | 3 | 114 | Regulation of beta-cell development (Reactome):REACT_13698 |
| 3.18533613032144e-06 | 0.000252039721311684 | 3 | 421 | Gene Expression (Reactome):REACT_71 |
| 1.29326205516739e-06 | 0.000116947840131565 | 3 | 312 | Diabetes pathways (Reactome):REACT_15380 |
| 1.23098667822397e-07 | 1.55842913463155e-05 | 3 | 143 | Influenza Infection (Reactome):REACT_6167 |
| 1.10547371417187e-07 | 1.55842913463155e-05 | 3 | 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:0005842 | cytosolic large ribosomal subunit (sensu Eukaryota) | 8.11246671004954e-08 |
| GO:0005830 | cytosolic ribosome (sensu Eukaryota) | 2.99701452344948e-07 |
| GO:0015934 | large ribosomal subunit | 5.54678852341937e-07 |
| GO:0044445 | cytosolic part | 2.49698689484997e-06 |
| GO:0033279 | ribosomal subunit | 3.28124645425421e-06 |
| GO:0005829 | cytosol | 4.4946882578473e-05 |
| GO:0003735 | structural constituent of ribosome | 9.91441963952388e-05 |
| GO:0005840 | ribosome | 0.000112771658049979 |
| GO:0003723 | RNA binding | 0.000152830307734731 |
| GO:0030529 | ribonucleoprotein complex | 0.000217462340567173 |
| GO:0006412 | translation | 0.000235913035980226 |
| GO:0009059 | macromolecule biosynthetic process | 0.000470758868352947 |
| GO:0044249 | cellular biosynthetic process | 0.000827081666316246 |
| GO:0009058 | biosynthetic process | 0.00155979504619136 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.00229977448464354 |
| GO:0043228 | non-membrane-bound organelle | 0.00229977448464354 |
| GO:0032991 | macromolecular complex | 0.00509120568496683 |
| GO:0044446 | intracellular organelle part | 0.00548130567723766 |
| GO:0044422 | organelle part | 0.00548130567723766 |
| GO:0000049 | tRNA binding | 0.00588633108744147 |
| GO:0044444 | cytoplasmic part | 0.00681719258441986 |
| GO:0019843 | rRNA binding | 0.00837260151835178 |
| GO:0010467 | gene expression | 0.0104299359727179 |
| GO:0044267 | cellular protein metabolic process | 0.0107018979530247 |
| GO:0044260 | cellular macromolecule metabolic process | 0.0107018979530247 |
| GO:0019538 | protein metabolic process | 0.0114328712142776 |
| GO:0003676 | nucleic acid binding | 0.0142031328827836 |
| GO:0005737 | cytoplasm | 0.0221219764203332 |
| GO:0005730 | nucleolus | 0.0290011854976768 |
| GO:0005515 | protein binding | 0.0357886869663508 |
| GO:0006605 | protein targeting | 0.0357886869663508 |
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 |
|---|---|---|
| native cell | 4.19e-19 | 722 |
| animal cell | 9.05e-15 | 679 |
| eukaryotic cell | 9.05e-15 | 679 |
| hematopoietic oligopotent progenitor cell | 2.75e-11 | 161 |
| hematopoietic multipotent progenitor cell | 2.75e-11 | 161 |
| classical monocyte | 2.85e-11 | 42 |
| CD14-positive, CD16-negative classical monocyte | 2.85e-11 | 42 |
| hematopoietic cell | 6.29e-11 | 177 |
| hematopoietic stem cell | 8.07e-11 | 168 |
| angioblastic mesenchymal cell | 8.07e-11 | 168 |
| stem cell | 1.92e-10 | 441 |
| hematopoietic lineage restricted progenitor cell | 4.07e-10 | 120 |
| nongranular leukocyte | 4.40e-10 | 115 |
| multi fate stem cell | 1.80e-09 | 427 |
| somatic stem cell | 8.06e-09 | 433 |
| somatic cell | 1.48e-08 | 588 |
| connective tissue cell | 1.58e-08 | 361 |
| defensive cell | 1.71e-08 | 48 |
| phagocyte | 1.71e-08 | 48 |
| mesenchymal cell | 9.03e-08 | 354 |
| nucleate cell | 2.87e-07 | 55 |
| leukocyte | 6.30e-07 | 136 |
| lymphoid lineage restricted progenitor cell | 6.54e-07 | 52 |
| lymphocyte | 6.77e-07 | 53 |
| common lymphoid progenitor | 6.77e-07 | 53 |
| Ontology term | p-value | n |
|---|---|---|
| connective tissue | 2.52e-08 | 371 |
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 | 0.178364 |
| MA0004.1 | 0.826076 |
| MA0006.1 | 0.639288 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 1.24048 |
| MA0017.1 | 0.686276 |
| MA0019.1 | 0.990656 |
| MA0024.1 | 1.21731 |
| MA0025.1 | 1.46617 |
| MA0027.1 | 2.95767 |
| MA0028.1 | 1.58389 |
| 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 | 0.190716 |
| MA0056.1 | 0 |
| MA0057.1 | 0.333427 |
| MA0058.1 | 0.716037 |
| MA0059.1 | 0.714521 |
| MA0060.1 | 0.492218 |
| 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 | 0.0185922 |
| MA0074.1 | 0.935474 |
| MA0076.1 | 1.74184 |
| 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 | 0.31555 |
| MA0106.1 | 0.986396 |
| MA0107.1 | 0.556367 |
| 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 | 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 | 0.440097 |
| MA0140.1 | 0.894983 |
| MA0141.1 | 0.712476 |
| MA0142.1 | 1.12317 |
| MA0143.1 | 1.00455 |
| MA0144.1 | 0.531867 |
| MA0145.1 | 0.273764 |
| MA0146.1 | 1.16674 |
| MA0147.1 | 0.565108 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 1.141 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 0.195278 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 1.20011 |
| 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 | 0.312019 |
| MA0155.1 | 0.711948 |
| MA0156.1 | 1.60572 |
| 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 | 0.09178 |
| 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 |
|---|---|---|---|---|
| BCL3#602 | 2 | 23.0314018691589 | 0.00246467476084291 | 0.0138540456053645 |
| BCLAF1#9774 | 2 | 14.4350984067479 | 0.00620114743554613 | 0.0273867404017677 |
| E2F4#1874 | 3 | 12.6680603152844 | 0.000491798700629898 | 0.00437466693595826 |
| ELF1#1997 | 3 | 4.25809795880754 | 0.0129517987505461 | 0.0462673727496334 |
| ELK4#2005 | 3 | 16.235681658468 | 0.000233604395574599 | 0.00255818490819079 |
| EP300#2033 | 3 | 6.7739417262232 | 0.00321688050010379 | 0.0167606776029104 |
| GABPB1#2553 | 3 | 7.06768383618217 | 0.00283221282541742 | 0.0154227788348595 |
| GTF2B#2959 | 3 | 31.9438299343242 | 3.06634405746243e-05 | 0.00062817949591471 |
| GTF2F1#2962 | 3 | 12.7396608767577 | 0.000483552504743859 | 0.00434274142599913 |
| IRF1#3659 | 3 | 7.6371637535639 | 0.00224469274729724 | 0.0128168752848383 |
| JUNB#3726 | 2 | 20.4070884398808 | 0.00313146219943874 | 0.0164493904359311 |
| JUND#3727 | 3 | 6.99466394187103 | 0.00292184504273499 | 0.0156891812040205 |
| KAT2A#2648 | 2 | 410.726666666667 | 7.8689746933917e-06 | 0.000222356019481368 |
| MAX#4149 | 3 | 6.45255550900712 | 0.00372191383426551 | 0.0186701709383696 |
| MEF2A#4205 | 2 | 12.495487273096 | 0.00823502947802974 | 0.032485674925626 |
| MYC#4609 | 3 | 5.2222818716094 | 0.00702084375574015 | 0.029475013104705 |
| NFKB1#4790 | 3 | 5.48806342419384 | 0.00604938181565543 | 0.0269777269501361 |
| POU2F2#5452 | 3 | 9.10612405774252 | 0.00132416519268213 | 0.00882824695553967 |
| REST#5978 | 3 | 9.65002871612802 | 0.00111263624711459 | 0.00768180187825746 |
| RFX5#5993 | 3 | 12.0479108271951 | 0.000571724605031258 | 0.00484976819565136 |
| SIN3A#25942 | 3 | 5.40888472681514 | 0.00631896197799152 | 0.0277032184543471 |
| SIX5#147912 | 3 | 17.086715355459 | 0.000200406054632501 | 0.00239860278933804 |
| SMC3#9126 | 2 | 10.0299552299552 | 0.012665637976747 | 0.0457553291128841 |
| SP1#6667 | 3 | 5.6983813781409 | 0.00540396270171217 | 0.0246736233542064 |
| TAF7#6879 | 3 | 11.4330694049239 | 0.000669018198194583 | 0.00543451750806907 |
| TCF12#6938 | 3 | 10.6344649021864 | 0.000831352399020207 | 0.00629673023433689 |
| YY1#7528 | 3 | 4.91117074985386 | 0.00844145534180826 | 0.0329687429207252 |
| ZNF143#7702 | 3 | 13.5008765522279 | 0.000406280496299717 | 0.00389315797348804 |
| ZZZ3#26009 | 2 | 159.608808290155 | 5.21262599582697e-05 | 0.000886791735426247 |
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.
