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Coexpression cluster:C4509: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190896816082422!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280937675608938!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327195485866751!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323937974933997!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000372291028466556!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000853737067812664!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109080086670108!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445937926779064!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157458500731785!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295712978305269!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173547885669704!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667469135593398!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310432996940586!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631459005100155!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190981785966896!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014075803202572!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243579928260226!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.0039035445035001
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190896816082422!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280937675608938!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327195485866751!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323937974933997!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000372291028466556!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000853737067812664!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109080086670108!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445937926779064!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157458500731785!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295712978305269!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173547885669704!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667469135593398!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310432996940586!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631459005100155!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190981785966896!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014075803202572!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243579928260226!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.0039035445035001
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}}
}}

Revision as of 16:47, 26 November 2012


Full id: C4509_CD14_renal_Whole_serous_signet_small_optic



Phase1 CAGE Peaks

Hg19::chr5:60140009..60140050,-p2@ELOVL7
Hg19::chr5:60140059..60140075,-p3@ELOVL7
Hg19::chr5:60140089..60140118,-p1@ELOVL7


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell1.38e-08253
endo-epithelial cell7.83e-0842
endodermal cell1.34e-0758
Uber Anatomy
Ontology termp-valuen
adult organism1.20e-37114
neural tube1.17e-2156
neural rod1.17e-2156
future spinal cord1.17e-2156
neural keel1.17e-2156
regional part of nervous system5.03e-2053
regional part of brain5.03e-2053
ecto-epithelium1.74e-19104
neural plate2.34e-1782
presumptive neural plate2.34e-1782
regional part of forebrain3.56e-1741
forebrain3.56e-1741
anterior neural tube3.56e-1741
future forebrain3.56e-1741
central nervous system1.90e-1681
neurectoderm2.65e-1686
organ3.61e-16503
brain5.72e-1668
future brain5.72e-1668
nervous system6.06e-1589
pre-chordal neural plate1.32e-1461
brain grey matter2.95e-1434
gray matter2.95e-1434
telencephalon3.32e-1434
regional part of telencephalon4.30e-1332
cerebral hemisphere5.24e-1332
organ system subdivision1.55e-12223
embryo2.23e-12592
ectoderm-derived structure2.41e-12171
ectoderm2.41e-12171
presumptive ectoderm2.41e-12171
developing anatomical structure2.54e-11581
regional part of cerebral cortex2.13e-1022
cerebral cortex2.10e-0925
pallium2.10e-0925
neocortex2.45e-0920
multi-cellular organism3.50e-09656
structure with developmental contribution from neural crest3.25e-08132
anatomical system4.98e-08624
anatomical group7.37e-08625
embryonic structure9.69e-08564
germ layer4.23e-07560
germ layer / neural crest4.23e-07560
embryonic tissue4.23e-07560
presumptive structure4.23e-07560
germ layer / neural crest derived structure4.23e-07560
epiblast (generic)4.23e-07560
organ part8.13e-07218
Disease
Ontology termp-valuen
carcinoma5.00e-11106
cell type cancer2.70e-08143


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#90536.336201576962630.003930750035764890.0190896816082422
CTCF#1066435.360256373075030.0064925092527670.0280937675608938
E2F1#186934.907389214879320.008460985347239390.0327195485866751
E2F6#187635.017155731697390.00791769806886330.0323937974933997
FOSL1#8061339.7135797163731.59554825631833e-050.000372291028466556
GATA3#2625327.2365163572064.94721007899563e-050.000853737067812664
HMGN3#932438.178547723350590.001827766942164210.0109080086670108
JUN#3725312.51282919233630.0005103313992726250.00445937926779064
JUND#372736.994663941871030.002921845042734990.0157458500731785
MYC#460935.22228187160940.007020843755740150.0295712978305269
PAX5#507936.669565531177830.003370290999677260.0173547885669704
RAD21#5885310.35503389545630.0009004912073565420.00667469135593398
SMC3#9126315.04493284493280.0002935825420371870.00310432996940586
TCF12#6938310.63446490218640.0008313523990202070.00631459005100155
USF1#739136.361499277207960.00388404057290560.0190981785966896
ZBTB7A#5134137.35190930787590.002516255860282270.014075803202572
ZEB1#6935316.88843201754390.0002075486917327580.00243579928260226
ZNF143#7702313.50087655222790.0004062804962997170.0039035445035001



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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