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Coexpression cluster:C1606: Difference between revisions

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|tf_chipseq_enrich=E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00322428997675529!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135117855578586!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00136702383198618
|tf_chipseq_enrich=E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00322428997675529!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135117855578586!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00136702383198618
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}}
}}

Revision as of 14:59, 26 November 2012


Full id: C1606_occipital_parietal_uterus_medulloblastoma_cervix_glioma_lung



Phase1 CAGE Peaks

Hg19::chr11:106889099..106889110,-p5@GUCY1A2
Hg19::chr11:106889125..106889143,-p2@GUCY1A2
Hg19::chr11:106889187..106889209,-p1@GUCY1A2
Hg19::chr11:106889216..106889227,-p6@GUCY1A2
Hg19::chr11:106889252..106889264,-p4@GUCY1A2


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 organism2.09e-47114
central nervous system5.19e-3581
neural tube2.19e-3456
neural rod2.19e-3456
future spinal cord2.19e-3456
neural keel2.19e-3456
regional part of nervous system1.99e-3253
regional part of brain1.99e-3253
brain8.50e-3268
future brain8.50e-3268
nervous system1.03e-3189
neural plate3.65e-3082
presumptive neural plate3.65e-3082
structure with developmental contribution from neural crest1.07e-29132
neurectoderm3.10e-2986
regional part of forebrain1.11e-2541
forebrain1.11e-2541
anterior neural tube1.11e-2541
future forebrain1.11e-2541
brain grey matter8.95e-2434
gray matter8.95e-2434
telencephalon2.88e-2334
ecto-epithelium3.77e-23104
organ system subdivision4.15e-23223
cerebral hemisphere1.78e-2232
anatomical cluster2.44e-22373
regional part of telencephalon3.76e-2232
pre-chordal neural plate4.73e-2161
ectoderm-derived structure1.09e-19171
ectoderm1.09e-19171
presumptive ectoderm1.09e-19171
regional part of cerebral cortex5.33e-1922
multi-tissue structure8.22e-18342
neocortex2.05e-1720
cerebral cortex6.15e-1725
pallium6.15e-1725
tube4.08e-15192
organ part2.02e-13218
epithelium7.55e-13306
cell layer2.33e-12309
anatomical conduit2.58e-12240
organ5.29e-12503
multi-cellular organism9.09e-11656
developing anatomical structure1.53e-10581
embryo1.57e-10592
embryonic structure3.50e-10564
germ layer3.98e-10560
germ layer / neural crest3.98e-10560
embryonic tissue3.98e-10560
presumptive structure3.98e-10560
germ layer / neural crest derived structure3.98e-10560
epiblast (generic)3.98e-10560
posterior neural tube9.77e-1015
chordal neural plate9.77e-1015
anatomical system2.29e-09624
anatomical group2.97e-09625
neural nucleus2.41e-089
nucleus of brain2.41e-089
basal ganglion4.97e-089
nuclear complex of neuraxis4.97e-089
aggregate regional part of brain4.97e-089
collection of basal ganglia4.97e-089
cerebral subcortex4.97e-089
primary circulatory organ5.02e-0827
segmental subdivision of hindbrain6.43e-0812
hindbrain6.43e-0812
presumptive hindbrain6.43e-0812
primordium2.30e-07160
segmental subdivision of nervous system5.08e-0713
telencephalic nucleus9.60e-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
E2F6#187655.017155731697390.0003144978599297790.00322428997675529
TAF1#687253.343046285745290.002394600090870310.0135117855578586
USF1#739156.361499277207969.59569864925045e-050.00136702383198618



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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