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Coexpression cluster:C4691: Difference between revisions

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|tf_chipseq_enrich=NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246654664523054
|tf_chipseq_enrich=NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246654664523054
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}}
}}

Revision as of 16:53, 26 November 2012


Full id: C4691_teratocarcinoma_carcinoid_merkel_retinoblastoma_testicular_carcinosarcoma_small



Phase1 CAGE Peaks

Hg19::chr7:64035038..64035062,+p2@uc003ttc.1
Hg19::chr7:64035065..64035085,+p1@uc003ttc.1
Hg19::chr7:64035097..64035108,+p3@uc003ttc.1


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
neural plate8.27e-1982
presumptive neural plate8.27e-1982
pre-chordal neural plate6.69e-1861
structure with developmental contribution from neural crest1.01e-17132
neurectoderm2.95e-1786
ecto-epithelium1.21e-14104
brain4.21e-1468
future brain4.21e-1468
ectoderm-derived structure9.40e-14171
ectoderm9.40e-14171
presumptive ectoderm9.40e-14171
central nervous system1.54e-1381
organ part4.19e-13218
regional part of nervous system6.17e-1353
regional part of brain6.17e-1353
cell layer7.83e-13309
neural tube9.48e-1356
neural rod9.48e-1356
future spinal cord9.48e-1356
neural keel9.48e-1356
telencephalon9.53e-1334
nervous system9.90e-1289
epithelium1.37e-11306
cerebral hemisphere1.43e-1132
regional part of telencephalon2.08e-1132
brain grey matter2.18e-1134
gray matter2.18e-1134
nephron epithelium6.66e-1115
renal tubule6.66e-1115
nephron tubule6.66e-1115
nephron6.66e-1115
uriniferous tubule6.66e-1115
nephrogenic mesenchyme6.66e-1115
regional part of forebrain2.64e-1041
forebrain2.64e-1041
anterior neural tube2.64e-1041
future forebrain2.64e-1041
multi-tissue structure3.40e-10342
excretory tube5.46e-1016
kidney epithelium5.46e-1016
nephron tubule epithelium7.17e-1010
cortex of kidney8.14e-1012
renal parenchyma8.14e-1012
eye8.94e-1021
visual system8.94e-1021
anatomical cluster2.89e-09373
camera-type eye3.67e-0920
simple eye3.67e-0920
immature eye3.67e-0920
ocular region3.67e-0920
eyeball of camera-type eye3.67e-0920
optic cup3.67e-0920
optic vesicle3.67e-0920
eye primordium3.67e-0920
cortex7.26e-0915
anterior segment of eyeball1.31e-0814
cerebral cortex3.64e-0825
pallium3.64e-0825
sense organ5.10e-0824
sensory system5.10e-0824
entire sense organ system5.10e-0824
face5.74e-0822
kidney7.77e-0826
kidney mesenchyme7.77e-0826
upper urinary tract7.77e-0826
kidney rudiment7.77e-0826
kidney field7.77e-0826
parenchyma2.75e-0715
vasculature of eye3.32e-076
uvea3.32e-076
vasculature of head3.32e-076
tube3.62e-07192
cavitated compound organ8.33e-0731


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
NFYB#4801316.75979325353650.0002123649923296180.00246654664523054



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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