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Coexpression cluster:C2202: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:05, 8 August 2012


Full id: C2202_heart_left_Hepatocyte_diaphragm_liver_pancreas_tongue



Phase1 CAGE Peaks

Hg19::chr12:21927609..21927617,-p9@KCNJ8
Hg19::chr12:21927622..21927664,-p1@KCNJ8
Hg19::chr12:21927670..21927685,-p4@KCNJ8
Hg19::chr12:21927687..21927708,-p3@KCNJ8


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 organism1.18e-32115
organism subdivision2.54e-23365
multi-tissue structure1.73e-18347
epithelium2.27e-15309
cell layer6.38e-15312
neural tube2.76e-1457
neural rod2.76e-1457
future spinal cord2.76e-1457
neural keel2.76e-1457
central nervous system5.77e-1482
regional part of nervous system7.34e-1494
nervous system7.34e-1494
multi-cellular organism8.13e-14659
muscle tissue1.54e-1363
musculature1.54e-1363
musculature of body1.54e-1363
tube1.75e-13194
neural plate3.84e-1386
presumptive neural plate3.84e-1386
regional part of brain6.33e-1359
skeletal muscle tissue1.30e-1261
striated muscle tissue1.30e-1261
myotome1.30e-1261
brain3.30e-1269
future brain3.30e-1269
anatomical conduit5.25e-12241
neurectoderm5.61e-1290
anatomical cluster1.05e-11286
trunk1.49e-11216
dermomyotome1.72e-1170
anterior neural tube4.45e-1142
regional part of forebrain1.71e-1041
forebrain1.71e-1041
future forebrain1.71e-1041
gray matter1.06e-0934
brain grey matter1.06e-0934
telencephalon1.41e-0934
anatomical group2.51e-09626
regional part of telencephalon2.80e-0933
anatomical system2.89e-09625
somite5.58e-0983
paraxial mesoderm5.58e-0983
presomitic mesoderm5.58e-0983
presumptive segmental plate5.58e-0983
trunk paraxial mesoderm5.58e-0983
presumptive paraxial mesoderm5.58e-0983
cerebral hemisphere5.71e-0932
trunk mesenchyme8.80e-09143
pre-chordal neural plate4.45e-0861
embryo4.47e-08612
multilaminar epithelium5.54e-0882
tissue8.73e-08787
mesenchyme1.24e-07238
entire embryonic mesenchyme1.24e-07238
embryonic structure2.10e-07605
developing anatomical structure2.10e-07605
unilaminar epithelium2.57e-07138
germ layer4.03e-07604
embryonic tissue4.03e-07604
presumptive structure4.03e-07604
epiblast (generic)4.03e-07604
adipose tissue5.14e-0714
ectoderm-derived structure6.68e-07169
cerebral cortex7.03e-0725
pallium7.03e-0725


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


No analysis results for this cluster

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.