Coexpression cluster:C43: Difference between revisions
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{{Coexpression_clusters | {{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0408567533019575,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.30398133462819,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0633281735501667,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.3965562150662,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C43_ductus_seminal_duodenum_temporal_gall_prostate_bladder|gostat_on_coexpression_clusters=GO:0016324!apical plasma membrane!0.0227850847922863!359;10568;50506$GO:0005624!membrane fraction!0.0227850847922863!11283;359;10568;23305;6578;1811$GO:0045177!apical part of cell!0.0227850847922863!359;10568;50506$GO:0003002!regionalization!0.0227850847922863!658;6926;2018$GO:0005100!Rho GTPase activator activity!0.038153331909274!395;10928$GO:0007389!pattern specification process!0.038153331909274!658;6926;2018$GO:0046660!female sex differentiation!0.038153331909274!658;6926$GO:0046545!development of primary female sexual characteristics!0.038153331909274!658;6926$GO:0000267!cell fraction!0.038153331909274!11283;359;10568;23305;6578;1811$GO:0048736!appendage development!0.038153331909274!658;6926$GO:0060173!limb development!0.038153331909274!658;6926$GO:0035107!appendage morphogenesis!0.038153331909274!658;6926$GO:0035108!limb morphogenesis!0.038153331909274!658;6926$GO:0030141!secretory granule!0.038153331909274!6406;6407$GO:0007588!excretion!0.0398367282860395!359;1811$GO:0005550!pheromone binding!0.0398367282860395!392399$GO:0032275!luteinizing hormone secretion!0.0398367282860395!6926$GO:0004603!phenylethanolamine N-methyltransferase activity!0.0398367282860395!5409$GO:0009952!anterior/posterior pattern formation!0.0465077853848852!6926;2018$GO:0051234!establishment of localization!0.0465077853848852!29986;359;9429;22841;10568;405753;6578;10928;288;392399;6926;1811$GO:0045137!development of primary sexual characteristics!0.0465077853848852!658;6926$GO:0001550!ovarian cumulus expansion!0.0465077853848852!658$GO:0022605!oogenesis stage!0.0465077853848852!658$GO:0017160!Ral GTPase binding!0.0465077853848852!10928$GO:0001547!antral ovarian follicle growth!0.0465077853848852!658$GO:0048165!fused antrum stage, oogenesis!0.0465077853848852!658$GO:0008393!fatty acid (omega-1)-hydroxylase activity!0.0465077853848852!11283$GO:0030540!female genitalia development!0.0465077853848852!6926$GO:0009651!response to salt stress!0.0465077853848852!359$GO:0048609!reproductive process in a multicellular organism!0.0465077853848852!658;6406$GO:0032504!multicellular organism reproduction!0.0465077853848852!658;6406$GO:0015103!inorganic anion transmembrane transporter activity!0.047749213512135!10568;1811$GO:0043089!positive regulation of Cdc42 GTPase activity!0.047749213512135!10928$GO:0030277!maintenance of gastrointestinal epithelium!0.047749213512135!4588$GO:0042335!cuticle development!0.047749213512135!50506$GO:0045662!negative regulation of myoblast differentiation!0.047749213512135!6926$GO:0035117!embryonic arm morphogenesis!0.047749213512135!6926$GO:0016565!general transcriptional repressor activity!0.047749213512135!6926$GO:0035140!arm morphogenesis!0.047749213512135!6926$GO:0001758!retinal dehydrogenase activity!0.047749213512135!8854$GO:0042910!xenobiotic transporter activity!0.047749213512135!9429$GO:0016174!NAD(P)H oxidase activity!0.047749213512135!50506$GO:0008559!xenobiotic-transporting ATPase 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transport of small molecules 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Latest revision as of 10:16, 17 September 2013
Full id: C43_ductus_seminal_duodenum_temporal_gall_prostate_bladder
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 |
---|---|---|---|---|
2.53205911108454e-05 | 0.0160279341731651 | 6 | 401 | Transmembrane transport of small molecules (Reactome):REACT_15518 |
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:0016324 | apical plasma membrane | 0.0227850847922863 |
GO:0005624 | membrane fraction | 0.0227850847922863 |
GO:0045177 | apical part of cell | 0.0227850847922863 |
GO:0003002 | regionalization | 0.0227850847922863 |
GO:0005100 | Rho GTPase activator activity | 0.038153331909274 |
GO:0007389 | pattern specification process | 0.038153331909274 |
GO:0046660 | female sex differentiation | 0.038153331909274 |
GO:0046545 | development of primary female sexual characteristics | 0.038153331909274 |
GO:0000267 | cell fraction | 0.038153331909274 |
GO:0048736 | appendage development | 0.038153331909274 |
GO:0060173 | limb development | 0.038153331909274 |
GO:0035107 | appendage morphogenesis | 0.038153331909274 |
GO:0035108 | limb morphogenesis | 0.038153331909274 |
GO:0030141 | secretory granule | 0.038153331909274 |
GO:0007588 | excretion | 0.0398367282860395 |
GO:0005550 | pheromone binding | 0.0398367282860395 |
GO:0032275 | luteinizing hormone secretion | 0.0398367282860395 |
GO:0004603 | phenylethanolamine N-methyltransferase activity | 0.0398367282860395 |
GO:0009952 | anterior/posterior pattern formation | 0.0465077853848852 |
GO:0051234 | establishment of localization | 0.0465077853848852 |
GO:0045137 | development of primary sexual characteristics | 0.0465077853848852 |
GO:0001550 | ovarian cumulus expansion | 0.0465077853848852 |
GO:0022605 | oogenesis stage | 0.0465077853848852 |
GO:0017160 | Ral GTPase binding | 0.0465077853848852 |
GO:0001547 | antral ovarian follicle growth | 0.0465077853848852 |
GO:0048165 | fused antrum stage, oogenesis | 0.0465077853848852 |
GO:0008393 | fatty acid (omega-1)-hydroxylase activity | 0.0465077853848852 |
GO:0030540 | female genitalia development | 0.0465077853848852 |
GO:0009651 | response to salt stress | 0.0465077853848852 |
GO:0048609 | reproductive process in a multicellular organism | 0.0465077853848852 |
GO:0032504 | multicellular organism reproduction | 0.0465077853848852 |
GO:0015103 | inorganic anion transmembrane transporter activity | 0.047749213512135 |
GO:0043089 | positive regulation of Cdc42 GTPase activity | 0.047749213512135 |
GO:0030277 | maintenance of gastrointestinal epithelium | 0.047749213512135 |
GO:0042335 | cuticle development | 0.047749213512135 |
GO:0045662 | negative regulation of myoblast differentiation | 0.047749213512135 |
GO:0035117 | embryonic arm morphogenesis | 0.047749213512135 |
GO:0016565 | general transcriptional repressor activity | 0.047749213512135 |
GO:0035140 | arm morphogenesis | 0.047749213512135 |
GO:0001758 | retinal dehydrogenase activity | 0.047749213512135 |
GO:0042910 | xenobiotic transporter activity | 0.047749213512135 |
GO:0016174 | NAD(P)H oxidase activity | 0.047749213512135 |
GO:0008559 | xenobiotic-transporting ATPase activity | 0.047749213512135 |
GO:0035005 | phosphatidylinositol-4-phosphate 3-kinase activity | 0.047749213512135 |
GO:0005549 | odorant binding | 0.047749213512135 |
GO:0051179 | localization | 0.0478004503973717 |
GO:0005886 | plasma membrane | 0.0478004503973717 |
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><br>uberon_data<br><br>
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 | 4.82164e-17 |
MA0004.1 | 0.025833 |
MA0006.1 | 0.0724677 |
MA0007.1 | 0.164461 |
MA0009.1 | 2.00214 |
MA0014.1 | 3.85731e-16 |
MA0017.1 | 0.3821 |
MA0019.1 | 0.00108573 |
MA0024.1 | 6.55836e-05 |
MA0025.1 | 0.0624703 |
MA0027.1 | 0.842496 |
MA0028.1 | 0.00964281 |
MA0029.1 | 0.479152 |
MA0030.1 | 1.24741 |
MA0031.1 | 0.250894 |
MA0038.1 | 0.0108249 |
MA0040.1 | 3.42376 |
MA0041.1 | 0.000330497 |
MA0042.1 | 0.0455059 |
MA0043.1 | 0.000497292 |
MA0046.1 | 3.04301 |
MA0048.1 | 0.0039805 |
MA0050.1 | 0.00296852 |
MA0051.1 | 0.00975309 |
MA0052.1 | 0.363827 |
MA0055.1 | 0.0138686 |
MA0056.1 | 0 |
MA0057.1 | 0.00103345 |
MA0058.1 | 0.00310973 |
MA0059.1 | 0.0345843 |
MA0060.1 | 0.18157 |
MA0061.1 | 0.00336091 |
MA0063.1 | 0 |
MA0066.1 | 0.841956 |
MA0067.1 | 0.019078 |
MA0068.1 | 8.23897e-05 |
MA0069.1 | 0.15301 |
MA0070.1 | 0.000315664 |
MA0071.1 | 0.681103 |
MA0072.1 | 0.0301403 |
MA0073.1 | 15.518 |
MA0074.1 | 3.58315 |
MA0076.1 | 5.11784e-09 |
MA0077.1 | 5.94611 |
MA0078.1 | 1.29111 |
MA0081.1 | 0.216901 |
MA0083.1 | 0.0465773 |
MA0084.1 | 0.221992 |
MA0087.1 | 3.1985 |
MA0088.1 | 0.0105696 |
MA0089.1 | 0 |
MA0090.1 | 0.0262748 |
MA0091.1 | 0.00496371 |
MA0092.1 | 1.44084 |
MA0093.1 | 0.0426521 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.117386 |
MA0101.1 | 0.000637351 |
MA0103.1 | 0.242987 |
MA0105.1 | 0.00126295 |
MA0106.1 | 0.00654716 |
MA0107.1 | 0.000133696 |
MA0108.2 | 1.48847 |
MA0109.1 | 0 |
MA0111.1 | 0.00520845 |
MA0113.1 | 0.97089 |
MA0114.1 | 0.257183 |
MA0115.1 | 0.0503206 |
MA0116.1 | 0.00105095 |
MA0117.1 | 0.000900736 |
MA0119.1 | 0.614894 |
MA0122.1 | 0.876846 |
MA0124.1 | 0.392932 |
MA0125.1 | 0.0163246 |
MA0130.1 | 0 |
MA0131.1 | 0.0137821 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.000806216 |
MA0136.1 | 0.153568 |
MA0139.1 | 0.036977 |
MA0140.1 | 0.263393 |
MA0141.1 | 1.76261 |
MA0142.1 | 0.00655072 |
MA0143.1 | 0.301946 |
MA0144.1 | 0.201648 |
MA0145.1 | 0.000893072 |
MA0146.1 | 2.6506e-12 |
MA0147.1 | 0.00866985 |
MA0148.1 | 0.76092 |
MA0149.1 | 2.63822e-07 |
MA0062.2 | 5.3038e-15 |
MA0035.2 | 0.936214 |
MA0039.2 | 0 |
MA0138.2 | 1.0957 |
MA0002.2 | 10.0634 |
MA0137.2 | 0.00039867 |
MA0104.2 | 0.000451312 |
MA0047.2 | 0.210453 |
MA0112.2 | 0.00710322 |
MA0065.2 | 1.73453 |
MA0150.1 | 0.133441 |
MA0151.1 | 0 |
MA0152.1 | 0.00188156 |
MA0153.1 | 3.85505 |
MA0154.1 | 0.0644471 |
MA0155.1 | 0.188987 |
MA0156.1 | 2.01377e-06 |
MA0157.1 | 0.0225872 |
MA0158.1 | 0 |
MA0159.1 | 0.037488 |
MA0160.1 | 4.4475 |
MA0161.1 | 0 |
MA0162.1 | 1.28614e-05 |
MA0163.1 | 6.05522e-05 |
MA0164.1 | 0.255251 |
MA0080.2 | 0.105367 |
MA0018.2 | 0.0798534 |
MA0099.2 | 0.000749503 |
MA0079.2 | 0 |
MA0102.2 | 0.0740995 |
MA0258.1 | 2.74057 |
MA0259.1 | 0.261904 |
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 |
---|---|---|---|---|
GATA3#2625 | 27 | 1.74262071479754 | 0.0042133097766613 | 0.020056237910881 |
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