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Coexpression cluster:C2693: Difference between revisions

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|tf_chipseq_enrich=SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.83011123491334e-06
|tf_chipseq_enrich=SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.83011123491334e-06
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}}
}}

Revision as of 15:39, 26 November 2012


Full id: C2693_anaplastic_nonsmall_bronchogenic_ovary_small_medulloblastoma_glassy



Phase1 CAGE Peaks

Hg19::chr2:233352519..233352525,-p3@ECEL1
Hg19::chr2:233352531..233352550,-p1@ECEL1
Hg19::chr2:233352555..233352566,-p2@ECEL1
Hg19::chr2:233352573..233352580,-p4@ECEL1


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>disease_data<br>

Cell Type
Ontology termp-valuen
embryonic stem cell6.56e-135
Uber Anatomy
Ontology termp-valuen
central nervous system4.32e-2081
nervous system1.03e-1889
neural tube1.25e-1856
neural rod1.25e-1856
future spinal cord1.25e-1856
neural keel1.25e-1856
regional part of nervous system3.14e-1653
regional part of brain3.14e-1653
adult organism2.31e-15114
neurectoderm1.15e-1486
neural plate1.57e-1482
presumptive neural plate1.57e-1482
brainstem4.11e-146
brain6.38e-1468
future brain6.38e-1468
organ system subdivision2.16e-11223
regional part of forebrain3.24e-1141
forebrain3.24e-1141
anterior neural tube3.24e-1141
future forebrain3.24e-1141
ecto-epithelium5.87e-11104
regional part of diencephalon3.02e-104
pre-chordal neural plate1.14e-0961
posterior neural tube2.51e-0915
chordal neural plate2.51e-0915
diencephalon8.54e-097
future diencephalon8.54e-097
neural nucleus1.15e-089
nucleus of brain1.15e-089
segmental subdivision of nervous system2.94e-0813
medulla oblongata4.14e-083
myelencephalon4.14e-083
future myelencephalon4.14e-083
ectoderm-derived structure6.41e-08171
ectoderm6.41e-08171
presumptive ectoderm6.41e-08171
structure with developmental contribution from neural crest8.21e-08132
anatomical cluster1.04e-07373
pons1.12e-073
Disease
Ontology termp-valuen
lung small cell carcinoma4.74e-104
bronchus cancer8.26e-097
bronchogenic carcinoma8.26e-097
lung cancer3.03e-0715


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
SUZ12#23512450.11578091106291.5827390373096e-078.83011123491334e-06



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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