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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C488_biphenotypic_acute_skeletal_hippocampus_Monocytederived_diaphragm_small
|full_id=C488_biphenotypic_acute_skeletal_hippocampus_Monocytederived_diaphragm_small
|id=C488
|id=C488

Revision as of 18:02, 12 September 2012


Full id: C488_biphenotypic_acute_skeletal_hippocampus_Monocytederived_diaphragm_small



Phase1 CAGE Peaks

Hg19::chr10:124894877..124894895,+p@chr10:124894877..124894895
+
Hg19::chr10:124894958..124894963,-p@chr10:124894958..124894963
-
Hg19::chr10:124907645..124907660,+p1@HMX2
Hg19::chr10:124907828..124907837,+p6@HMX2
Hg19::chr10:124907876..124907888,+p5@HMX2
Hg19::chr10:71332711..71332719,+p@chr10:71332711..71332719
+
Hg19::chr10:7453445..7453459,-p1@SFMBT2
Hg19::chr10:7453559..7453566,+p1@AK123101
Hg19::chr15:43531113..43531125,-p@chr15:43531113..43531125
-
Hg19::chr15:43531148..43531194,-p@chr15:43531148..43531194
-
Hg19::chr17:56368264..56368268,+p@chr17:56368264..56368268
+
Hg19::chr17:79792942..79792953,-p2@PPP1R27
Hg19::chr17:79793013..79793019,-p3@PPP1R27
Hg19::chr1:246269774..246269792,-p@chr1:246269774..246269792
-
Hg19::chr1:246271474..246271493,-p@chr1:246271474..246271493
-
Hg19::chr1:246271512..246271521,-p@chr1:246271512..246271521
-
Hg19::chr1:246271543..246271558,-p@chr1:246271543..246271558
-
Hg19::chr5:134788086..134788121,-p3@TIFAB
Hg19::chr8:48626488..48626489,+p@chr8:48626488..48626489
+


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>


Uber Anatomy
Ontology termp-valuen
adult organism2.16e-23115
central nervous system2.85e-1382
neural tube2.13e-1157
neural rod2.13e-1157
future spinal cord2.13e-1157
neural keel2.13e-1157
brain3.50e-1169
future brain3.50e-1169
anterior neural tube4.90e-1142
regional part of nervous system7.46e-1194
nervous system7.46e-1194
regional part of forebrain9.06e-1141
forebrain9.06e-1141
future forebrain9.06e-1141
regional part of brain1.96e-0959
telencephalon8.92e-0934
gray matter1.52e-0834
brain grey matter1.52e-0834
regional part of telencephalon2.55e-0833
cerebral hemisphere1.18e-0732
bone element3.00e-0786
hematopoietic system4.35e-07102
blood island4.35e-07102
bone marrow4.94e-0780
regional part of cerebral cortex5.67e-0722
Disease
Ontology termp-valuen
myeloid leukemia2.04e-1831
leukemia8.88e-1739
hematologic cancer3.46e-1551
immune system cancer3.46e-1551


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.