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Coexpression cluster:C2320: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00511645571180078!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00816333091406765!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106377863039411!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101346022986507!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00247877096055952!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129172296251082!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195766956686716!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321714431627035!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346164496810944
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00511645571180078!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00816333091406765!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106377863039411!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101346022986507!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00247877096055952!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129172296251082!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195766956686716!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321714431627035!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346164496810944
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}}
}}

Revision as of 15:25, 26 November 2012


Full id: C2320_neuroblastoma_cerebellum_retinoblastoma_pituitary_rectum_putamen_pineal



Phase1 CAGE Peaks

Hg19::chr14:89259135..89259181,-p2@EML5
Hg19::chr14:89259211..89259225,-p3@EML5
Hg19::chr14:89259247..89259263,-p6@EML5
Hg19::chr14:89259268..89259310,-p1@EML5


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
lymphoid lineage restricted progenitor cell6.64e-0752
Uber Anatomy
Ontology termp-valuen
adult organism2.78e-36114
neural tube2.06e-3356
neural rod2.06e-3356
future spinal cord2.06e-3356
neural keel2.06e-3356
regional part of nervous system3.63e-3153
regional part of brain3.63e-3153
central nervous system5.38e-2781
nervous system5.43e-2789
regional part of forebrain7.28e-2741
forebrain7.28e-2741
anterior neural tube7.28e-2741
future forebrain7.28e-2741
brain6.03e-2568
future brain6.03e-2568
neural plate8.80e-2582
presumptive neural plate8.80e-2582
neurectoderm3.00e-2386
brain grey matter1.57e-2134
gray matter1.57e-2134
telencephalon2.22e-2134
cerebral hemisphere2.80e-2032
regional part of telencephalon5.27e-2032
pre-chordal neural plate9.18e-2061
ecto-epithelium3.32e-18104
regional part of cerebral cortex5.71e-1822
neocortex2.73e-1620
cerebral cortex9.58e-1525
pallium9.58e-1525
organ system subdivision3.87e-14223
structure with developmental contribution from neural crest2.84e-13132
ectoderm-derived structure3.65e-13171
ectoderm3.65e-13171
presumptive ectoderm3.65e-13171
neural nucleus2.06e-089
nucleus of brain2.06e-089
basal ganglion3.27e-089
nuclear complex of neuraxis3.27e-089
aggregate regional part of brain3.27e-089
collection of basal ganglia3.27e-089
cerebral subcortex3.27e-089
posterior neural tube8.57e-0815
chordal neural plate8.57e-0815
diencephalon5.48e-077
future diencephalon5.48e-077
telencephalic nucleus6.73e-077


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#90546.336201576962630.0006203100587215640.00511645571180078
CTCF#1066445.360256373075030.001211145381643620.00816333091406765
E2F1#186944.907389214879320.001724022357361790.0106377863039411
EGR1#195844.988179094810140.001615011500076050.0101346022986507
HMGN3#932448.178547723350590.0002234570284440470.00247877096055952
RAD21#5885410.35503389545638.6948481184721e-050.00129172296251082
REST#597837.237521537096020.004104697304192610.0195766956686716
TAF1#687243.343046285745290.008005664898701650.0321714431627035
ZBTB7A#5134147.35190930787590.000342223540015990.00346164496810944



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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