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Coexpression cluster:C895: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C895_Mesenchymal_Renal_Alveolar_Fibroblast_Pericytes_Trabecular_Osteoblast
|full_id=C895_Mesenchymal_Renal_Alveolar_Fibroblast_Pericytes_Trabecular_Osteoblast
|gostat_on_coexpression_clusters=GO:0009098!leucine biosynthetic process!0.00653479335923701!587$GO:0006549!isoleucine metabolic process!0.00653479335923701!587$GO:0006550!isoleucine catabolic process!0.00653479335923701!587$GO:0009082!branched chain family amino acid biosynthetic process!0.00980074736638496!587$GO:0006551!leucine metabolic process!0.00980074736638496!587$GO:0009301!snRNA transcription!0.00980074736638496!6618$GO:0006420!arginyl-tRNA aminoacylation!0.0130647783764645!55152$GO:0004814!arginine-tRNA ligase activity!0.0130647783764645!55152$GO:0004084!branched-chain-amino-acid transaminase activity!0.0130647783764645!587$GO:0009083!branched chain family amino acid catabolic process!0.017633557274085!587$GO:0006520!amino acid metabolic process!0.0261103347061558!587;55152$GO:0009081!branched chain family amino acid metabolic process!0.0261103347061558!587$GO:0007595!lactation!0.0295901655496141!587$GO:0006519!amino acid and derivative metabolic process!0.0295901655496141!587;55152$GO:0006383!transcription from RNA polymerase III promoter!0.0346414888684331!6618$GO:0009308!amine metabolic process!0.0346414888684331!587;55152$GO:0006807!nitrogen compound metabolic process!0.036932758980158!587;55152$GO:0019752!carboxylic acid metabolic process!0.0449410093543494!587;55152$GO:0006082!organic acid metabolic process!0.0449410093543494!587;55152$GO:0008483!transaminase activity!0.0449410093543494!587
|gostat_on_coexpression_clusters=GO:0009098!leucine biosynthetic process!0.00653479335923701!587$GO:0006549!isoleucine metabolic process!0.00653479335923701!587$GO:0006550!isoleucine catabolic process!0.00653479335923701!587$GO:0009082!branched chain family amino acid biosynthetic process!0.00980074736638496!587$GO:0006551!leucine metabolic process!0.00980074736638496!587$GO:0009301!snRNA transcription!0.00980074736638496!6618$GO:0006420!arginyl-tRNA aminoacylation!0.0130647783764645!55152$GO:0004814!arginine-tRNA ligase activity!0.0130647783764645!55152$GO:0004084!branched-chain-amino-acid transaminase activity!0.0130647783764645!587$GO:0009083!branched chain family amino acid catabolic process!0.017633557274085!587$GO:0006520!amino acid metabolic process!0.0261103347061558!587;55152$GO:0009081!branched chain family amino acid metabolic process!0.0261103347061558!587$GO:0007595!lactation!0.0295901655496141!587$GO:0006519!amino acid and derivative metabolic process!0.0295901655496141!587;55152$GO:0006383!transcription from RNA polymerase III promoter!0.0346414888684331!6618$GO:0009308!amine metabolic process!0.0346414888684331!587;55152$GO:0006807!nitrogen compound metabolic process!0.036932758980158!587;55152$GO:0019752!carboxylic acid metabolic process!0.0449410093543494!587;55152$GO:0006082!organic acid metabolic process!0.0449410093543494!587;55152$GO:0008483!transaminase activity!0.0449410093543494!587

Revision as of 18:40, 12 September 2012


Full id: C895_Mesenchymal_Renal_Alveolar_Fibroblast_Pericytes_Trabecular_Osteoblast



Phase1 CAGE Peaks

Hg19::chr12:53693466..53693537,+p1@C12orf10
Hg19::chr16:2933231..2933309,+p1@FLYWCH2
Hg19::chr17:42092313..42092389,-p1@TMEM101
Hg19::chr19:17530838..17530885,+p1@FAM125A
Hg19::chr19:17530888..17530938,+p2@FAM125A
Hg19::chr19:49314305..49314316,-p2@BCAT2
Hg19::chr19:7985198..7985257,+p1@SNAPC2
Hg19::chr3:49055991..49056026,-p1@DALRD3
Hg19::chr9:131133622..131133661,+p1@URM1


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

No results for this coexpression

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 IDGO nameFDR corrected p-value
GO:0009098leucine biosynthetic process0.00653479335923701
GO:0006549isoleucine metabolic process0.00653479335923701
GO:0006550isoleucine catabolic process0.00653479335923701
GO:0009082branched chain family amino acid biosynthetic process0.00980074736638496
GO:0006551leucine metabolic process0.00980074736638496
GO:0009301snRNA transcription0.00980074736638496
GO:0006420arginyl-tRNA aminoacylation0.0130647783764645
GO:0004814arginine-tRNA ligase activity0.0130647783764645
GO:0004084branched-chain-amino-acid transaminase activity0.0130647783764645
GO:0009083branched chain family amino acid catabolic process0.017633557274085
GO:0006520amino acid metabolic process0.0261103347061558
GO:0009081branched chain family amino acid metabolic process0.0261103347061558
GO:0007595lactation0.0295901655496141
GO:0006519amino acid and derivative metabolic process0.0295901655496141
GO:0006383transcription from RNA polymerase III promoter0.0346414888684331
GO:0009308amine metabolic process0.0346414888684331
GO:0006807nitrogen compound metabolic process0.036932758980158
GO:0019752carboxylic acid metabolic process0.0449410093543494
GO:0006082organic acid metabolic process0.0449410093543494
GO:0008483transaminase activity0.0449410093543494



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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.47e-28180
embryonic cell9.53e-22248
mesodermal cell5.31e-19119
contractile cell3.39e-1759
electrically responsive cell6.53e-1560
electrically active cell6.53e-1560
animal cell9.73e-15679
eukaryotic cell9.73e-15679
muscle cell2.01e-1454
muscle precursor cell4.60e-1457
myoblast4.60e-1457
multi-potent skeletal muscle stem cell4.60e-1457
somatic cell5.23e-13591
smooth muscle cell7.29e-1242
smooth muscle myoblast7.29e-1242
epithelial cell3.53e-10254
fibroblast3.23e-0975
vascular associated smooth muscle cell9.11e-0932
meso-epithelial cell3.22e-0844
epithelial cell of nephron4.82e-0816
kidney cell9.81e-0818
kidney epithelial cell9.81e-0818
native cell1.08e-07722
endothelial cell1.25e-0735
ectodermal cell3.37e-0771
kidney cortical cell8.64e-0713
renal cortical epithelial cell8.64e-0713
Uber Anatomy
Ontology termp-valuen
multilaminar epithelium5.05e-1582
dermomyotome5.96e-1570
somite8.37e-1583
paraxial mesoderm8.37e-1583
presomitic mesoderm8.37e-1583
presumptive segmental plate8.37e-1583
trunk paraxial mesoderm8.37e-1583
presumptive paraxial mesoderm8.37e-1583
vasculature7.23e-1479
vascular system7.23e-1479
mesenchyme3.77e-13238
entire embryonic mesenchyme3.77e-13238
trunk7.16e-13216
trunk mesenchyme9.34e-13143
skeletal muscle tissue2.11e-1261
striated muscle tissue2.11e-1261
myotome2.11e-1261
unilaminar epithelium3.47e-12138
splanchnic layer of lateral plate mesoderm9.62e-1284
epithelial tube1.35e-11118
muscle tissue1.81e-1163
musculature1.81e-1163
musculature of body1.81e-1163
vessel3.06e-1169
multi-tissue structure1.14e-10347
blood vessel3.24e-1060
epithelial tube open at both ends3.24e-1060
blood vasculature3.24e-1060
vascular cord3.24e-1060
artery7.43e-1042
arterial blood vessel7.43e-1042
arterial system7.43e-1042
organism subdivision2.00e-09365
cell layer2.27e-09312
epithelium5.92e-09309
cardiovascular system1.01e-08110
nephron epithelium4.82e-0816
nephron4.82e-0816
uriniferous tubule4.82e-0816
metanephric mesenchyme4.82e-0816
nephrogenic mesenchyme4.82e-0816
circulatory system5.07e-08113
excretory tube1.61e-0717
mesonephric epithelium1.61e-0717
mesonephric tubule1.61e-0717
nephric duct1.61e-0717
kidney epithelium1.61e-0717
renal duct1.61e-0717
mesonephric duct1.61e-0717
pronephric duct1.61e-0717
parenchyma5.11e-0717
mesonephros6.42e-0718
pronephros6.42e-0718
nephrogenic cord6.42e-0718
pronephric mesoderm6.42e-0718
rostral part of nephrogenic cord6.42e-0718
presumptive pronephric mesoderm6.42e-0718
systemic artery7.36e-0733
systemic arterial system7.36e-0733
cortex of kidney8.64e-0713
renal parenchyma8.64e-0713


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)

{{{tfbs_overrepresentation_jaspar}}}



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#promotersEnrichmentp-valueq-value
BCLAF1#9774614.43509840674797.2101191630514e-073.21527598321915e-05
CCNT2#90564.224134384641760.000840335063808250.0063381059961775
CHD2#110655.746679352287140.0007610423709220.00597612813358817
E2F1#186973.816858278239470.0003547577053237570.00355264550640597
E2F6#187673.902232235764630.0003067423599492730.00316216220814749
EGR1#195873.8796948515190.0003186557858542290.00326243423378393
ELF1#199794.258097958807542.17161853202127e-067.8234449074084e-05
ELK4#200559.019823143593359.04446507305493e-050.00132018852238265
ETS1#211388.647787486402081.01768374293787e-075.96441483887138e-06
FOS#235343.999091248397510.01211384991200480.0439291101027732
FOSL2#235535.643400201520560.01321558041905920.0467586558501971
GABPB1#255375.497087428141693.13640621886058e-050.000632849940285124
HEY1#2346294.040111043105713.4850025352467e-060.000115950997062323
HMGN3#932476.361092673717131.17234969197953e-050.000298050217820474
IRF1#365986.788590003167916.86477102732501e-073.09831383458426e-05
MAX#414964.301703672671410.0007597563851723660.00596782469246516
MXI1#460166.64104775250626.5621720999513e-050.0010635423524935
MYC#460963.48152124773960.002423669811459260.0136566307763147
NFYB#480135.586597751178820.01358500277111940.0479487700038166
NRF1#489968.140186298473942.03653511272495e-050.00045157896101461
POLR2A#543092.147453176558070.001029412892608020.0072859076369673
POLR3A#11128275.36269113149850.0003081865015822640.00317235265511039
REST#597844.288901651612450.009457025945962830.035662839240672
RFX5#599368.03194055146342.20018388626684e-050.000482538859508236
SIN3A#2594284.807897534946791.02597602607548e-050.000267946762158783
SIX5#147912611.3911435703062.88946640975924e-069.93000929150529e-05
SP1#666753.16576743230050.01119721686091820.0411190622973782
SRF#672257.665099034537670.0001964447812163450.00236147519629994
STAT3#677444.6753177765130.006946825355778890.0293815856045111
TAF1#687282.971596698440260.0004233749951234810.00395889167478747
TBP#690872.883043867741630.002187802002126050.0126161919993397
TCF7L2#693455.983431423965190.0006305154397321440.0051842546063758
THAP1#55145413.94184204571170.0001142867648675440.00156435064692023
TRIM28#1015536.196841681754170.0102278065029780.0380813505655799
USF1#739153.534166265115530.00692296754081810.0293091656327983
YY1#752884.365485110981212.17675027117712e-050.000479109845250721
ZBTB7A#5134175.718151683903472.40589727322203e-050.000524242656620145
ZEB1#693547.505969785575050.001215903324635610.00818272616287248
ZNF143#770257.500486973459950.0002177465175801830.00249164331648479



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.

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