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|ontology_enrichment_disease=DOID:0050687!1.20e-09!143;DOID:305!1.86e-07!106
|ontology_enrichment_disease=DOID:0050687!1.20e-09!143;DOID:305!1.86e-07!106
|ontology_enrichment_uberon=UBERON:0007023!8.42e-14!115;UBERON:0005743!1.63e-12!86;UBERON:0002346!1.97e-12!90;UBERON:0001017!4.86e-12!82;UBERON:0001049!8.26e-12!57;UBERON:0005068!8.26e-12!57;UBERON:0006241!8.26e-12!57;UBERON:0007135!8.26e-12!57;UBERON:0000924!8.44e-12!173;UBERON:0006601!8.44e-12!173;UBERON:0000955!1.19e-11!69;UBERON:0006238!1.19e-11!69;UBERON:0000073!3.64e-11!94;UBERON:0001016!3.64e-11!94;UBERON:0002780!9.32e-11!41;UBERON:0001890!9.32e-11!41;UBERON:0006240!9.32e-11!41;UBERON:0003075!1.30e-10!86;UBERON:0007284!1.30e-10!86;UBERON:0004121!2.51e-10!169;UBERON:0003080!2.69e-10!42;UBERON:0001893!1.19e-09!34;UBERON:0002791!2.53e-09!33;UBERON:0002616!2.55e-09!59;UBERON:0002020!5.08e-09!34;UBERON:0003528!5.08e-09!34;UBERON:0000033!6.92e-09!123;UBERON:0000153!9.96e-09!129;UBERON:0007811!9.96e-09!129;UBERON:0000062!1.26e-08!511;UBERON:0001869!2.17e-08!32;UBERON:0003056!2.65e-08!61
|ontology_enrichment_uberon=UBERON:0007023!8.42e-14!115;UBERON:0005743!1.63e-12!86;UBERON:0002346!1.97e-12!90;UBERON:0001017!4.86e-12!82;UBERON:0001049!8.26e-12!57;UBERON:0005068!8.26e-12!57;UBERON:0006241!8.26e-12!57;UBERON:0007135!8.26e-12!57;UBERON:0000924!8.44e-12!173;UBERON:0006601!8.44e-12!173;UBERON:0000955!1.19e-11!69;UBERON:0006238!1.19e-11!69;UBERON:0000073!3.64e-11!94;UBERON:0001016!3.64e-11!94;UBERON:0002780!9.32e-11!41;UBERON:0001890!9.32e-11!41;UBERON:0006240!9.32e-11!41;UBERON:0003075!1.30e-10!86;UBERON:0007284!1.30e-10!86;UBERON:0004121!2.51e-10!169;UBERON:0003080!2.69e-10!42;UBERON:0001893!1.19e-09!34;UBERON:0002791!2.53e-09!33;UBERON:0002616!2.55e-09!59;UBERON:0002020!5.08e-09!34;UBERON:0003528!5.08e-09!34;UBERON:0000033!6.92e-09!123;UBERON:0000153!9.96e-09!129;UBERON:0007811!9.96e-09!129;UBERON:0000062!1.26e-08!511;UBERON:0001869!2.17e-08!32;UBERON:0003056!2.65e-08!61
|pathway_enrichment=1.82684577066052e-05;0.0115639337282811;2;71;Melanoma (KEGG):05218
}}
}}

Revision as of 14:54, 13 July 2012


Full id: C1318_retina_Melanocyte_globus_caudate_eye_melanoma_nucleus



Phase1 CAGE Peaks

Hg19::chr10:63123003..63123038,-p@chr10:63123003..63123038
-
Hg19::chr3:69986115..69986119,+p12@MITF
Hg19::chr4:22341289..22341308,-p1@LOC100505912
Hg19::chr6:10412249..10412254,-p41@TFAP2A
Hg19::chr6:10412262..10412271,-p21@TFAP2A
Hg19::chr7:116311841..116311852,+p33@MET


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


p.valueFDRnGenesnPathwayName
1.82684577066052e-050.0115639337282811271Melanoma (KEGG):05218



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:0048012hepatocyte growth factor receptor signaling pathway0.00435652890615801
GO:0005008hepatocyte growth factor receptor activity0.00435652890615801
GO:0051450myoblast proliferation0.00435652890615801
GO:0016563transcription activator activity0.00909867646707665
GO:0007275multicellular organismal development0.00916255739815988
GO:0030318melanocyte differentiation0.014933592894531
GO:0050931pigment cell differentiation0.014933592894531
GO:0032502developmental process0.0175503814073968
GO:0045178basal part of cell0.0175503814073968
GO:0048066pigmentation during development0.0175503814073968
GO:0009925basal plasma membrane0.0175503814073968
GO:0032501multicellular organismal process0.0175503814073968
GO:0030317sperm motility0.0195928403967735
GO:0007595lactation0.0195928403967735
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0220380517978679
GO:0030534adult behavior0.0220380517978679
GO:0019861flagellum0.0257497172747369
GO:0001764neuron migration0.0257497172747369
GO:0048513organ development0.0257497172747369
GO:0046777protein amino acid autophosphorylation0.0285907117347742
GO:0016540protein autoprocessing0.0285907117347742
GO:0000187activation of MAPK activity0.0331598958932373
GO:0048609reproductive process in a multicellular organism0.0331598958932373
GO:0032504multicellular organism reproduction0.0331598958932373
GO:0043406positive regulation of MAP kinase activity0.0344377311136857
GO:0048731system development0.036895850629173
GO:0016323basolateral plasma membrane0.0391939630078132
GO:0065007biological regulation0.0391939630078132
GO:0043405regulation of MAP kinase activity0.0391939630078132
GO:0048869cellular developmental process0.0391939630078132
GO:0030154cell differentiation0.0391939630078132
GO:0016485protein processing0.0403175002874271
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0430321421924296
GO:0048856anatomical structure development0.0436787634291092
GO:0019199transmembrane receptor protein kinase activity0.0443602688604381
GO:0050954sensory perception of mechanical stimulus0.0443602688604381
GO:0007605sensory perception of sound0.0443602688604381
GO:0007420brain development0.0443602688604381
GO:0045860positive regulation of protein kinase activity0.0443602688604381
GO:0033674positive regulation of kinase activity0.0443602688604381
GO:0043283biopolymer metabolic process0.0443602688604381
GO:0007398ectoderm development0.0443602688604381
GO:0051347positive regulation of transferase activity0.0443602688604381
GO:0000165MAPKKK cascade0.0443602688604381
GO:0007517muscle development0.0497038261938837



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>


Cell Type
Ontology termp-valuen
neurecto-epithelial cell4.58e-1020
columnar/cuboidal epithelial cell7.05e-1027
melanocyte7.52e-0910
melanoblast7.52e-0910
epithelial cell5.37e-08254
ecto-epithelial cell6.98e-0833
Uber Anatomy
Ontology termp-valuen
adult organism8.42e-14115
neurectoderm1.97e-1290
central nervous system4.86e-1282
neural tube8.26e-1257
neural rod8.26e-1257
future spinal cord8.26e-1257
neural keel8.26e-1257
ectoderm8.44e-12173
presumptive ectoderm8.44e-12173
brain1.19e-1169
future brain1.19e-1169
regional part of nervous system3.64e-1194
nervous system3.64e-1194
regional part of forebrain9.32e-1141
forebrain9.32e-1141
future forebrain9.32e-1141
neural plate1.30e-1086
presumptive neural plate1.30e-1086
ectoderm-derived structure2.51e-10169
anterior neural tube2.69e-1042
telencephalon1.19e-0934
regional part of telencephalon2.53e-0933
regional part of brain2.55e-0959
gray matter5.08e-0934
brain grey matter5.08e-0934
head6.92e-09123
anterior region of body9.96e-09129
craniocervical region9.96e-09129
organ1.26e-08511
cerebral hemisphere2.17e-0832
pre-chordal neural plate2.65e-0861
Disease
Ontology termp-valuen
cell type cancer1.20e-09143
carcinoma1.86e-07106


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.