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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4698_spinal_heart_esophagus_trachea_duodenum_substantia_penis
|full_id=C4698_spinal_heart_esophagus_trachea_duodenum_substantia_penis
|gostat_on_coexpression_clusters=GO:0043034!costamere!0.00824159647213382!1756$GO:0043043!peptide biosynthetic process!0.00824159647213382!1756$GO:0016010!dystrophin-associated glycoprotein complex!0.0230639023484972!1756$GO:0006518!peptide metabolic process!0.0230639023484972!1756$GO:0005605!basal lamina!0.0230639023484972!1756$GO:0008307!structural constituent of muscle!0.0230639023484972!1756$GO:0030016!myofibril!0.023422404691628!1756$GO:0044449!contractile fiber part!0.023422404691628!1756$GO:0043292!contractile fiber!0.023422404691628!1756$GO:0005604!basement membrane!0.0243703490898033!1756$GO:0005200!structural constituent of cytoskeleton!0.0254440286675898!1756$GO:0044420!extracellular matrix part!0.0353517517207721!1756$GO:0003012!muscle system process!0.0353517517207721!1756$GO:0006936!muscle contraction!0.0353517517207721!1756$GO:0004867!serine-type endopeptidase inhibitor activity!0.0353517517207721!340267$GO:0007517!muscle development!0.0353517517207721!1756$GO:0004866!endopeptidase inhibitor activity!0.0485298345557758!340267$GO:0030414!protease inhibitor activity!0.0485298345557758!340267
|gostat_on_coexpression_clusters=GO:0043034!costamere!0.00824159647213382!1756$GO:0043043!peptide biosynthetic process!0.00824159647213382!1756$GO:0016010!dystrophin-associated glycoprotein complex!0.0230639023484972!1756$GO:0006518!peptide metabolic process!0.0230639023484972!1756$GO:0005605!basal lamina!0.0230639023484972!1756$GO:0008307!structural constituent of muscle!0.0230639023484972!1756$GO:0030016!myofibril!0.023422404691628!1756$GO:0044449!contractile fiber part!0.023422404691628!1756$GO:0043292!contractile fiber!0.023422404691628!1756$GO:0005604!basement membrane!0.0243703490898033!1756$GO:0005200!structural constituent of cytoskeleton!0.0254440286675898!1756$GO:0044420!extracellular matrix part!0.0353517517207721!1756$GO:0003012!muscle system process!0.0353517517207721!1756$GO:0006936!muscle contraction!0.0353517517207721!1756$GO:0004867!serine-type endopeptidase inhibitor activity!0.0353517517207721!340267$GO:0007517!muscle development!0.0353517517207721!1756$GO:0004866!endopeptidase inhibitor activity!0.0485298345557758!340267$GO:0030414!protease inhibitor activity!0.0485298345557758!340267

Revision as of 17:49, 12 September 2012


Full id: C4698_spinal_heart_esophagus_trachea_duodenum_substantia_penis



Phase1 CAGE Peaks

Hg19::chr7:7575477..7575491,-p2@COL28A1
Hg19::chr7:7575494..7575509,-p1@COL28A1
Hg19::chrX:31526382..31526422,-p10@DMD


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


GO IDGO nameFDR corrected p-value
GO:0043034costamere0.00824159647213382
GO:0043043peptide biosynthetic process0.00824159647213382
GO:0016010dystrophin-associated glycoprotein complex0.0230639023484972
GO:0006518peptide metabolic process0.0230639023484972
GO:0005605basal lamina0.0230639023484972
GO:0008307structural constituent of muscle0.0230639023484972
GO:0030016myofibril0.023422404691628
GO:0044449contractile fiber part0.023422404691628
GO:0043292contractile fiber0.023422404691628
GO:0005604basement membrane0.0243703490898033
GO:0005200structural constituent of cytoskeleton0.0254440286675898
GO:0044420extracellular matrix part0.0353517517207721
GO:0003012muscle system process0.0353517517207721
GO:0006936muscle contraction0.0353517517207721
GO:0004867serine-type endopeptidase inhibitor activity0.0353517517207721
GO:0007517muscle development0.0353517517207721
GO:0004866endopeptidase inhibitor activity0.0485298345557758
GO:0030414protease inhibitor activity0.0485298345557758



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 organism3.59e-65115
neural tube4.83e-2557
neural rod4.83e-2557
future spinal cord4.83e-2557
neural keel4.83e-2557
neural plate1.19e-2186
presumptive neural plate1.19e-2186
central nervous system8.78e-2182
neurectoderm3.95e-2090
regional part of brain1.15e-1859
regional part of nervous system1.34e-1794
nervous system1.34e-1794
anterior neural tube1.49e-1542
brain2.21e-1569
future brain2.21e-1569
regional part of forebrain1.29e-1441
forebrain1.29e-1441
future forebrain1.29e-1441
gray matter1.32e-1234
brain grey matter1.32e-1234
ectoderm-derived structure1.49e-12169
telencephalon1.65e-1234
brainstem2.40e-128
ectoderm6.12e-12173
presumptive ectoderm6.12e-12173
regional part of telencephalon9.30e-1233
anterior region of body2.10e-11129
craniocervical region2.10e-11129
posterior neural tube2.98e-1115
chordal neural plate2.98e-1115
multi-tissue structure3.19e-11347
anatomical conduit5.28e-11241
cerebral hemisphere1.61e-1032
head3.51e-10123
organ3.79e-10511
pre-chordal neural plate8.74e-1061
anatomical cluster1.61e-09286
tube2.12e-09194
cerebral cortex8.66e-0925
pallium8.66e-0925
compound organ1.63e-0869
multi-cellular organism2.90e-08659
anatomical system1.08e-07625
anatomical group1.23e-07626
embryo1.27e-07612
primary circulatory organ3.21e-0727
segmental subdivision of hindbrain3.96e-0712
hindbrain3.96e-0712
presumptive hindbrain3.96e-0712
embryonic structure4.76e-07605
developing anatomical structure4.76e-07605


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.