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Coexpression cluster:C4581: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115696157267988!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000859112236205523
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115696157267988!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000859112236205523
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}}
}}

Revision as of 16:49, 26 November 2012


Full id: C4581_Chondrocyte_salivary_submaxillary_parotid_dura_aorta_retina



Phase1 CAGE Peaks

Hg19::chr6:1626414..1626429,-p7@GMDS
Hg19::chr6:1626436..1626467,-p4@GMDS
Hg19::chr6:1626471..1626487,-p9@GMDS


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 organism4.46e-20114
articulation3.92e-168
skeletal joint3.92e-168
articular system3.92e-168
intervertebral cartilage7.04e-115
symphysis7.04e-115
nonsynovial joint7.04e-115
fibrous joint7.04e-115
cartilaginous joint7.04e-115
developing mesenchymal condensation7.04e-115
pre-cartilage condensation7.04e-115
cartilaginous condensation7.04e-115
cartilage element7.04e-115
post-cranial axial skeletal system7.04e-115
vertebral column7.04e-115
intervertebral disk7.04e-115
intervertebral joint7.04e-115
central nervous system1.67e-1081
anatomical cluster3.12e-10373
neural tube3.41e-0956
neural rod3.41e-0956
future spinal cord3.41e-0956
neural keel3.41e-0956
nervous system8.93e-0989
neural plate1.71e-0882
presumptive neural plate1.71e-0882
posterior neural tube1.83e-0815
chordal neural plate1.83e-0815
organ system subdivision2.21e-08223
brain3.35e-0868
future brain3.35e-0868
gland of diencephalon6.09e-084
neuroendocrine gland6.09e-084
neurectoderm8.25e-0886
multi-tissue structure1.61e-07342
brainstem1.84e-076
nucleus pulposus3.46e-073
axial mesoderm3.46e-073
notochord3.46e-073
chordamesoderm3.46e-073
gland of gut5.20e-0710
stratified squamous epithelium6.34e-073
layer of synovial tissue6.34e-073
synovial joint6.34e-073
synovial membrane of synovial joint6.34e-073
regional part of nervous system8.48e-0753
regional part of brain8.48e-0753
spinal cord9.59e-073
dorsal region element9.59e-073
dorsum9.59e-073


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)

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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
CEBPB#105137.971147625824820.001974187055288560.0115696157267988
MAFK#7975327.10073313782995.02195559325033e-050.000859112236205523



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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