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Coexpression cluster:C434: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C434_heart_left_Monocytederived_acute_skeletal_penis_seminal
|full_id=C434_heart_left_Monocytederived_acute_skeletal_penis_seminal
|id=C434
|id=C434

Revision as of 17:24, 12 September 2012


Full id: C434_heart_left_Monocytederived_acute_skeletal_penis_seminal



Phase1 CAGE Peaks

Hg19::chr14:84054028..84054030,-p@chr14:84054028..84054030
-
Hg19::chr17:22021434..22021440,+p@chr17:22021434..22021440
+
Hg19::chr4:117219365..117219385,+p@chr4:117219365..117219385
+
Hg19::chr4:156387212..156387216,-p@chr4:156387212..156387216
-
Hg19::chr4:93623091..93623118,+p@chr4:93623091..93623118
+
Hg19::chr8:32869035..32869038,+p@chr8:32869035..32869038
+
Hg19::chrM:1706..1717,+p5@uc004cos.3
Hg19::chrM:1746..1757,+p4@uc004cos.3
Hg19::chrM:2402..2413,+p3@AK026170
Hg19::chrM:2699..2710,+p4@AB462505
Hg19::chrM:2716..2771,+p1@AB462505
Hg19::chrM:2777..2784,+p6@AB462505
Hg19::chrM:2812..2839,+p2@AB462505
Hg19::chrM:2852..2863,+p5@AB462505
Hg19::chrM:2880..2896,+p3@AB462505
Hg19::chrM:694..705,+p@chrM:694..705
+
Hg19::chrM:719..730,+p@chrM:719..730
+
Hg19::chrM:732..757,+p@chrM:732..757
+
Hg19::chrM:783..794,+p@chrM:783..794
+
Hg19::chrM:808..819,+p@chrM:808..819
+
Hg19::chrM:9282..9333,+p1@HQ013247
Hg19::chrM:931..961,+p@chrM:931..961
+
Hg19::chrM:988..1012,+p@chrM:988..1012
+


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 organism2.06e-24115
neural tube4.55e-1257
neural rod4.55e-1257
future spinal cord4.55e-1257
neural keel4.55e-1257
gray matter4.48e-1134
brain grey matter4.48e-1134
anterior neural tube4.57e-1142
regional part of forebrain8.84e-1141
forebrain8.84e-1141
future forebrain8.84e-1141
telencephalon4.65e-1034
regional part of brain5.33e-1059
regional part of telencephalon5.47e-1033
cerebral hemisphere7.29e-1032
regional part of cerebral cortex8.90e-0922
brain4.27e-0869
future brain4.27e-0869
central nervous system9.35e-0882
neocortex9.45e-0820
cerebral cortex1.59e-0725
pallium1.59e-0725
neurectoderm1.79e-0790
neural plate7.50e-0786
presumptive neural plate7.50e-0786


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.