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Coexpression cluster:C4353: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190692866492591!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115559983111356!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280600527146589!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326784086638931!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323583043871655!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321775809621855!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464006898225948!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582975812798703!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445490647012986!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015727995795186!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270377621194521!POU5F1#5460;3:335.439201451906:2.63510205045339e-08:1.82256571554505e-06!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666664784894803!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00375871293069439!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140645033873171!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243333832688342
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190692866492591!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115559983111356!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280600527146589!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326784086638931!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323583043871655!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321775809621855!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464006898225948!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582975812798703!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445490647012986!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015727995795186!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270377621194521!POU5F1#5460;3:335.439201451906:2.63510205045339e-08:1.82256571554505e-06!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666664784894803!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00375871293069439!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140645033873171!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243333832688342
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}}
}}

Revision as of 16:41, 26 November 2012


Full id: C4353_heart_penis_aorta_smooth_sacrococcigeal_Mast_mesodermal



Phase1 CAGE Peaks

Hg19::chr3:99594980..99594993,-p3@FILIP1L
Hg19::chr3:99594998..99595024,-p1@FILIP1L
Hg19::chr3:99595037..99595051,-p2@FILIP1L


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

No GOStat results

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
mesodermal cell6.54e-10121
muscle precursor cell9.14e-0858
myoblast9.14e-0858
multi-potent skeletal muscle stem cell9.14e-0858
muscle cell1.53e-0755
fibroblast2.56e-0776
contractile cell5.94e-0759
Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.61e-17656
anatomical system1.63e-15624
anatomical group2.20e-15625
trunk mesenchyme2.58e-13122
mesenchyme1.45e-12160
entire embryonic mesenchyme1.45e-12160
organism subdivision5.78e-12264
unilaminar epithelium2.83e-11148
epithelium7.51e-11306
cell layer1.04e-10309
anatomical cluster2.28e-10373
epithelial tube3.04e-10117
embryonic structure3.12e-10564
multilaminar epithelium3.55e-1083
multi-tissue structure4.13e-10342
muscle tissue4.87e-1064
musculature4.87e-1064
musculature of body4.87e-1064
developing anatomical structure7.83e-10581
trunk9.80e-10199
epithelial vesicle1.77e-0978
anatomical conduit3.09e-09240
skeletal muscle tissue3.41e-0962
striated muscle tissue3.41e-0962
myotome3.41e-0962
somite3.75e-0971
presomitic mesoderm3.75e-0971
presumptive segmental plate3.75e-0971
dermomyotome3.75e-0971
trunk paraxial mesoderm3.75e-0971
germ layer4.04e-09560
germ layer / neural crest4.04e-09560
embryonic tissue4.04e-09560
presumptive structure4.04e-09560
germ layer / neural crest derived structure4.04e-09560
epiblast (generic)4.04e-09560
paraxial mesoderm4.22e-0972
presumptive paraxial mesoderm4.22e-0972
dense mesenchyme tissue4.58e-0973
embryo2.11e-08592
splanchnic layer of lateral plate mesoderm2.14e-0883
mesoderm5.41e-08315
mesoderm-derived structure5.41e-08315
presumptive mesoderm5.41e-08315
organ6.57e-08503
vasculature7.83e-0878
vascular system7.83e-0878
vessel7.22e-0768


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
CCNT2#90536.336201576962630.003930750035764890.0190692866492591
CEBPB#105137.971147625824820.001974187055288560.0115559983111356
CTCF#1066435.360256373075030.0064925092527670.0280600527146589
E2F1#186934.907389214879320.008460985347239390.0326784086638931
E2F6#187635.017155731697390.00791769806886330.0323583043871655
EGR1#195834.988179094810140.008056488137383440.0321775809621855
ELF1#199734.258097958807540.01295179875054610.0464006898225948
FOXA1#3169311.08141974938550.000734755275698670.00582975812798703
JUN#3725312.51282919233630.0005103313992726250.00445490647012986
JUND#372736.994663941871030.002921845042734990.015727995795186
NFKB1#479035.488063424193840.006049381815655430.0270377621194521
POU5F1#54603335.4392014519062.63510205045339e-081.82256571554505e-06
RAD21#5885310.35503389545630.0009004912073565420.00666664784894803
SRF#6722313.79717826216780.0003806615025800190.00375871293069439
ZBTB7A#5134137.35190930787590.002516255860282270.0140645033873171
ZEB1#6935316.88843201754390.0002075486917327580.00243333832688342



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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