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Coexpression cluster:C2679: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512820092003653!CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.96280048635183e-06!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997983727996421!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161106602710669!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378726504777638!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444421998893938!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120154143684997!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304716601856077!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249344258258518
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512820092003653!CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.96280048635183e-06!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997983727996421!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161106602710669!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378726504777638!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444421998893938!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120154143684997!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304716601856077!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249344258258518
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}}
}}

Revision as of 15:39, 26 November 2012


Full id: C2679_optic_pons_pituitary_ductus_seminal_paracentral_parietal



Phase1 CAGE Peaks

Hg19::chr2:191272875..191272890,+p7@MFSD6
Hg19::chr2:191272893..191272923,+p2@MFSD6
Hg19::chr2:191272963..191272983,+p6@MFSD6
Hg19::chr2:191273052..191273121,+p1@MFSD6


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>

Uber Anatomy
Ontology termp-valuen
adult organism2.83e-45114
neural tube4.32e-2156
neural rod4.32e-2156
future spinal cord4.32e-2156
neural keel4.32e-2156
regional part of nervous system1.45e-1953
regional part of brain1.45e-1953
regional part of forebrain1.61e-1741
forebrain1.61e-1741
anterior neural tube1.61e-1741
future forebrain1.61e-1741
brain2.01e-1568
future brain2.01e-1568
central nervous system4.77e-1581
telencephalon1.74e-1334
brain grey matter1.84e-1334
gray matter1.84e-1334
nervous system2.43e-1389
organ system subdivision3.48e-13223
regional part of telencephalon2.78e-1232
cerebral hemisphere2.85e-1232
ecto-epithelium6.60e-12104
regional part of cerebral cortex7.02e-1222
organ1.15e-11503
neural plate1.22e-1182
presumptive neural plate1.22e-1182
neocortex8.26e-1120
neurectoderm6.58e-1086
ectoderm-derived structure1.71e-09171
ectoderm1.71e-09171
presumptive ectoderm1.71e-09171
cerebral cortex2.04e-0925
pallium2.04e-0925
hematopoietic system3.60e-0998
blood island3.60e-0998
pre-chordal neural plate6.71e-0961
bone marrow1.65e-0776
hemolymphoid system3.41e-07108


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#90546.336201576962630.0006203100587215640.00512820092003653
CTBP2#1488462.71700033932816.45042639894877e-083.96280048635183e-06
E2F6#187645.017155731697390.00157802193473060.00997983727996421
ELF1#199744.258097958807540.003041525565781240.0161106602710669
GABPB1#255335.300762877136630.01012678824234270.0378726504777638
PAX5#507946.669565531177830.0005052774169483260.00444421998893938
TCF12#6938410.63446490218647.8163066689251e-050.00120154143684997
ZEB1#6935416.88843201754391.22862303393937e-050.000304716601856077
ZNF263#1012748.221841637010680.0002187871180958320.00249344258258518



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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