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Coexpression cluster:C3503: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3503_osteoclastoma_acute_small_hepatoblastoma_stomach_sacrococcigeal_heart
|full_id=C3503_osteoclastoma_acute_small_hepatoblastoma_stomach_sacrococcigeal_heart
|id=C3503
|id=C3503

Revision as of 16:26, 12 September 2012


Full id: C3503_osteoclastoma_acute_small_hepatoblastoma_stomach_sacrococcigeal_heart



Phase1 CAGE Peaks

Hg19::chr15:63340604..63340622,+p7@TPM1
Hg19::chr15:63340647..63340728,+p2@TPM1
Hg19::chr15:63340734..63340769,+p4@TPM1


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
adult organism7.14e-32115
anatomical cluster6.35e-18286
multi-cellular organism3.74e-17659
multi-tissue structure1.06e-16347
anatomical conduit1.29e-16241
neural tube3.90e-1457
neural rod3.90e-1457
future spinal cord3.90e-1457
neural keel3.90e-1457
epithelium8.65e-14309
cell layer9.04e-14312
regional part of brain9.19e-1459
anatomical system1.78e-13625
anatomical group3.68e-13626
embryo4.64e-13612
central nervous system4.98e-1382
tube5.72e-13194
brain7.61e-1369
future brain7.61e-1369
anterior neural tube1.30e-1142
regional part of nervous system1.31e-1194
nervous system1.31e-1194
embryonic structure2.19e-11605
developing anatomical structure2.19e-11605
germ layer4.17e-11604
embryonic tissue4.17e-11604
presumptive structure4.17e-11604
epiblast (generic)4.17e-11604
regional part of forebrain4.64e-1141
forebrain4.64e-1141
future forebrain4.64e-1141
neural plate8.15e-1186
presumptive neural plate8.15e-1186
subdivision of digestive tract1.13e-10129
endodermal part of digestive tract1.13e-10129
organism subdivision1.61e-10365
gray matter3.73e-1034
brain grey matter3.73e-1034
digestive system8.98e-10155
digestive tract8.98e-10155
primitive gut8.98e-10155
organ1.08e-09511
cerebral hemisphere1.19e-0932
telencephalon1.43e-0934
regional part of telencephalon2.95e-0933
neurectoderm5.19e-0990
ectoderm-derived structure1.79e-08169
regional part of cerebral cortex1.90e-0822
endoderm-derived structure2.00e-08169
endoderm2.00e-08169
presumptive endoderm2.00e-08169
mixed endoderm/mesoderm-derived structure9.55e-08130
neocortex1.75e-0720
organ part2.01e-07219
ectoderm2.20e-07173
presumptive ectoderm2.20e-07173
cerebral cortex2.44e-0725
pallium2.44e-0725
mesenchyme9.91e-07238
entire embryonic mesenchyme9.91e-07238


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
BCL3#602334.54710280373832.42397750207122e-050.000526753612856463
BCLAF1#9774321.65264761012189.8473954032885e-050.00139092795310258
CCNT2#90536.336201576962630.003930750035764890.0189679620655754
CTBP2#1488362.71700033932814.049570681927e-060.000129416497077654
CTCF#1066435.360256373075030.0064925092527670.027900718999701
CTCFL#140690319.74647435897440.0001298372005551160.00171472779321899
E2F1#186934.907389214879320.008460985347239390.0324563596811994
EGR1#195834.988179094810140.008056488137383440.0319879700646361
ELF1#199734.258097958807540.01295179875054610.0461238077439998
ELK4#2005316.2356816584680.0002336043955745990.00255470256224246
EP300#203336.77394172622320.003216880500103790.0167231350199273
ETS1#211339.728760922202340.001085840092584840.00760998882227001
GABPB1#255337.067683836182170.002832212825417420.0153866768244783
GATA1#2623313.56030814380040.0004009615963782630.00387453998558007
GTF2B#2959331.94382993432423.06634405746243e-050.000627072463319599
GTF2F1#2962312.73966087675770.0004835525047438590.00433342543701252
HDAC2#3066313.41562023662630.0004140761399857210.00390656711688967
HMGN3#932438.178547723350590.001827766942164210.0108540485399834
JUND#372736.994663941871030.002921845042734990.0156481500650325
NR3C1#2908314.9730233311730.0002978331194675480.0030840167721665
NRF1#4899312.21027944771090.0005492172401020010.00470431389641704
PAX5#507936.669565531177830.003370290999677260.017265405489542
RAD21#5885310.35503389545630.0009004912073565420.0066309244310167
REST#597839.650028716128020.001112636247114590.00766406918694108
RXRA#6256213.38307809275550.007196434429465730.0298225702475586
SMARCB1#6598318.25271578115740.000164397760679890.00202781832144172
SMC3#9126315.04493284493280.0002935825420371870.00308558590196455
STAT1#6772320.70658749719920.0001125992441046670.00154652189045861
TCF7L2#6934310.77017656313730.0008003181298398380.00612699202186944
TFAP2A#7020316.5186343730450.0002218033880766340.00247806205042101
TFAP2C#7022310.80922860986020.0007916746575753130.00614322829054968
THAP1#55145331.36914460285133.23800758564397e-050.000645863778145666
TRIM28#10155318.59052504526250.0001555969297255280.00196759749892292
USF1#739136.361499277207960.00388404057290560.0189962214757745
USF2#7392312.99219738506960.0004558979393427810.0042113501580595
YY1#752834.911170749853860.008441455341808260.0328667295870531
ZBTB7A#5134137.35190930787590.002516255860282270.0139881431730462
ZEB1#6935316.88843201754390.0002075486917327580.00242408608989907
ZNF143#7702313.50087655222790.0004062804962997170.00388424832964538



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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