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Coexpression cluster:C4587: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000477!2.35e-12!286;UBERON:0000468!4.72e-11!659;UBERON:0004111!6.44e-11!241;UBERON:0000480!1.05e-09!626;UBERON:0000467!1.20e-09!625;UBERON:0000025!1.21e-08!194;UBERON:0000062!4.23e-08!511;UBERON:0000923!1.26e-07!604;UBERON:0005291!1.26e-07!604;UBERON:0006598!1.26e-07!604;UBERON:0002532!1.26e-07!604;UBERON:0000475!1.51e-07!365;UBERON:0000481!1.63e-07!347;UBERON:0000926!1.72e-07!448;UBERON:0004120!1.72e-07!448;UBERON:0006603!1.72e-07!448;UBERON:0001737!2.21e-07!9;UBERON:0002050!2.28e-07!605;UBERON:0005423!2.28e-07!605;UBERON:0000922!2.61e-07!612;UBERON:0003914!4.44e-07!118;UBERON:0001041!8.60e-07!98
|ontology_enrichment_uberon=UBERON:0000477!2.35e-12!286;UBERON:0000468!4.72e-11!659;UBERON:0004111!6.44e-11!241;UBERON:0000480!1.05e-09!626;UBERON:0000467!1.20e-09!625;UBERON:0000025!1.21e-08!194;UBERON:0000062!4.23e-08!511;UBERON:0000923!1.26e-07!604;UBERON:0005291!1.26e-07!604;UBERON:0006598!1.26e-07!604;UBERON:0002532!1.26e-07!604;UBERON:0000475!1.51e-07!365;UBERON:0000481!1.63e-07!347;UBERON:0000926!1.72e-07!448;UBERON:0004120!1.72e-07!448;UBERON:0006603!1.72e-07!448;UBERON:0001737!2.21e-07!9;UBERON:0002050!2.28e-07!605;UBERON:0005423!2.28e-07!605;UBERON:0000922!2.61e-07!612;UBERON:0003914!4.44e-07!118;UBERON:0001041!8.60e-07!98
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190976741247325!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115702649757173!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172278838632649!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327401574168334!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324039526867829!EBF1#1879;3:8.906466846569:0.0014152328356098:0.0091867426265307!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322194740409799!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464612526519298!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00256275309552684!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764796691593389!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154736072020177!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109111261316198!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.012865408069091!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.017359924132733!REST#5978;3:9.65002871612802:0.00111263624711459:0.00770829963598014!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278071069826594!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247710876318521!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155326277308774!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545317970820605!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000722527421928903!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.0063173467113847!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249299656127159!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618458445377426!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140803282143174!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.011002538416711
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}}
}}

Revision as of 14:33, 5 September 2012


Full id: C4587_left_large_Hepatocyte_skeletal_liver_mature_parotid



Phase1 CAGE Peaks

Hg19::chr6:3000171..3000185,+p3@NQO2
Hg19::chr6:3000195..3000214,+p6@NQO2
Hg19::chr6:3000218..3000229,+p7@NQO2


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
anatomical cluster2.35e-12286
multi-cellular organism4.72e-11659
anatomical conduit6.44e-11241
anatomical group1.05e-09626
anatomical system1.20e-09625
tube1.21e-08194
organ4.23e-08511
germ layer1.26e-07604
embryonic tissue1.26e-07604
presumptive structure1.26e-07604
epiblast (generic)1.26e-07604
organism subdivision1.51e-07365
multi-tissue structure1.63e-07347
mesoderm1.72e-07448
mesoderm-derived structure1.72e-07448
presumptive mesoderm1.72e-07448
larynx2.21e-079
embryonic structure2.28e-07605
developing anatomical structure2.28e-07605
embryo2.61e-07612
epithelial tube4.44e-07118
foregut8.60e-0798


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#90536.336201576962630.003930750035764890.0190976741247325
CEBPB#105137.971147625824820.001974187055288560.0115702649757173
CTCFL#140690319.74647435897440.0001298372005551160.00172278838632649
E2F1#186934.907389214879320.008460985347239390.0327401574168334
E2F6#187635.017155731697390.00791769806886330.0324039526867829
EBF1#187938.9064668465690.00141523283560980.0091867426265307
EGR1#195834.988179094810140.008056488137383440.0322194740409799
ELF1#199734.258097958807540.01295179875054610.0464612526519298
ELK4#2005316.2356816584680.0002336043955745990.00256275309552684
ETS1#211339.728760922202340.001085840092584840.00764796691593389
GABPB1#255337.067683836182170.002832212825417420.0154736072020177
HMGN3#932438.178547723350590.001827766942164210.0109111261316198
IRF1#365937.63716375356390.002244692747297240.012865408069091
PAX5#507936.669565531177830.003370290999677260.017359924132733
REST#597839.650028716128020.001112636247114590.00770829963598014
SIN3A#2594235.408884726815140.006318961977991520.0278071069826594
SP1#666735.69838137814090.005403962701712170.0247710876318521
STAT1#6772320.70658749719920.0001125992441046670.00155326277308774
TAF7#6879311.43306940492390.0006690181981945830.00545317970820605
TAL1#6886329.86861667744023.75103522793067e-050.000722527421928903
TCF12#6938310.63446490218640.0008313523990202070.0063173467113847
TFAP2A#7020316.5186343730450.0002218033880766340.00249299656127159
TFAP2C#7022310.80922860986020.0007916746575753130.00618458445377426
ZBTB7A#5134137.35190930787590.002516255860282270.0140803282143174
ZNF263#1012738.221841637010680.001799043925565870.011002538416711



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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