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Coexpression cluster:C2085: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.17e-72!115;UBERON:0001049!2.55e-37!57;UBERON:0005068!2.55e-37!57;UBERON:0006241!2.55e-37!57;UBERON:0007135!2.55e-37!57;UBERON:0002616!7.29e-31!59;UBERON:0003075!1.19e-26!86;UBERON:0007284!1.19e-26!86;UBERON:0003080!1.20e-26!42;UBERON:0001017!5.54e-26!82;UBERON:0002780!5.74e-26!41;UBERON:0001890!5.74e-26!41;UBERON:0006240!5.74e-26!41;UBERON:0005743!2.17e-25!86;UBERON:0000955!9.26e-25!69;UBERON:0006238!9.26e-25!69;UBERON:0002346!1.27e-24!90;UBERON:0000073!2.01e-23!94;UBERON:0001016!2.01e-23!94;UBERON:0002020!1.29e-19!34;UBERON:0003528!1.29e-19!34;UBERON:0001893!1.92e-19!34;UBERON:0002791!7.16e-19!33;UBERON:0001869!2.36e-17!32;UBERON:0003056!6.38e-16!61;UBERON:0000153!1.70e-14!129;UBERON:0007811!1.70e-14!129;UBERON:0004121!4.79e-14!169;UBERON:0000033!8.79e-14!123;UBERON:0000924!2.94e-13!173;UBERON:0006601!2.94e-13!173;UBERON:0002619!4.49e-13!22;UBERON:0000956!5.67e-12!25;UBERON:0000203!5.67e-12!25;UBERON:0003076!1.18e-11!15;UBERON:0003057!1.18e-11!15;UBERON:0001950!2.29e-11!20;UBERON:0000025!8.68e-11!194;UBERON:0004111!1.06e-10!241;UBERON:0002308!8.26e-10!9;UBERON:0000125!8.26e-10!9;UBERON:0002298!1.40e-09!8;UBERON:0002420!2.00e-09!9;UBERON:0007245!2.00e-09!9;UBERON:0010009!2.00e-09!9;UBERON:0010011!2.00e-09!9;UBERON:0000454!2.00e-09!9;UBERON:0000477!2.23e-09!286;UBERON:0004732!2.80e-09!13;UBERON:0001894!2.31e-08!7;UBERON:0006222!2.31e-08!7;UBERON:0004733!2.58e-08!12;UBERON:0002028!2.58e-08!12;UBERON:0007277!2.58e-08!12;UBERON:0009663!5.76e-08!7;UBERON:0000062!1.35e-07!511;UBERON:0001871!1.62e-07!7
|ontology_enrichment_uberon=UBERON:0007023!9.17e-72!115;UBERON:0001049!2.55e-37!57;UBERON:0005068!2.55e-37!57;UBERON:0006241!2.55e-37!57;UBERON:0007135!2.55e-37!57;UBERON:0002616!7.29e-31!59;UBERON:0003075!1.19e-26!86;UBERON:0007284!1.19e-26!86;UBERON:0003080!1.20e-26!42;UBERON:0001017!5.54e-26!82;UBERON:0002780!5.74e-26!41;UBERON:0001890!5.74e-26!41;UBERON:0006240!5.74e-26!41;UBERON:0005743!2.17e-25!86;UBERON:0000955!9.26e-25!69;UBERON:0006238!9.26e-25!69;UBERON:0002346!1.27e-24!90;UBERON:0000073!2.01e-23!94;UBERON:0001016!2.01e-23!94;UBERON:0002020!1.29e-19!34;UBERON:0003528!1.29e-19!34;UBERON:0001893!1.92e-19!34;UBERON:0002791!7.16e-19!33;UBERON:0001869!2.36e-17!32;UBERON:0003056!6.38e-16!61;UBERON:0000153!1.70e-14!129;UBERON:0007811!1.70e-14!129;UBERON:0004121!4.79e-14!169;UBERON:0000033!8.79e-14!123;UBERON:0000924!2.94e-13!173;UBERON:0006601!2.94e-13!173;UBERON:0002619!4.49e-13!22;UBERON:0000956!5.67e-12!25;UBERON:0000203!5.67e-12!25;UBERON:0003076!1.18e-11!15;UBERON:0003057!1.18e-11!15;UBERON:0001950!2.29e-11!20;UBERON:0000025!8.68e-11!194;UBERON:0004111!1.06e-10!241;UBERON:0002308!8.26e-10!9;UBERON:0000125!8.26e-10!9;UBERON:0002298!1.40e-09!8;UBERON:0002420!2.00e-09!9;UBERON:0007245!2.00e-09!9;UBERON:0010009!2.00e-09!9;UBERON:0010011!2.00e-09!9;UBERON:0000454!2.00e-09!9;UBERON:0000477!2.23e-09!286;UBERON:0004732!2.80e-09!13;UBERON:0001894!2.31e-08!7;UBERON:0006222!2.31e-08!7;UBERON:0004733!2.58e-08!12;UBERON:0002028!2.58e-08!12;UBERON:0007277!2.58e-08!12;UBERON:0009663!5.76e-08!7;UBERON:0000062!1.35e-07!511;UBERON:0001871!1.62e-07!7
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}}
}}

Revision as of 17:58, 8 August 2012


Full id: C2085_Melanocyte_melanoma_retina_substantia_spinal_left_vagina



Phase1 CAGE Peaks

Hg19::chr10:97181989..97182006,-p8@SORBS1
Hg19::chr10:97182014..97182028,-p17@SORBS1
Hg19::chr10:97182043..97182098,-p5@SORBS1
Hg19::chr19:29374516..29374529,+p@chr19:29374516..29374529
+


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>


Cell Type
Ontology termp-valuen
melanocyte2.10e-1110
melanoblast2.10e-1110
pigment cell2.64e-0714
Uber Anatomy
Ontology termp-valuen
adult organism9.17e-72115
neural tube2.55e-3757
neural rod2.55e-3757
future spinal cord2.55e-3757
neural keel2.55e-3757
regional part of brain7.29e-3159
neural plate1.19e-2686
presumptive neural plate1.19e-2686
anterior neural tube1.20e-2642
central nervous system5.54e-2682
regional part of forebrain5.74e-2641
forebrain5.74e-2641
future forebrain5.74e-2641
brain9.26e-2569
future brain9.26e-2569
neurectoderm1.27e-2490
regional part of nervous system2.01e-2394
nervous system2.01e-2394
gray matter1.29e-1934
brain grey matter1.29e-1934
telencephalon1.92e-1934
regional part of telencephalon7.16e-1933
cerebral hemisphere2.36e-1732
pre-chordal neural plate6.38e-1661
anterior region of body1.70e-14129
craniocervical region1.70e-14129
ectoderm-derived structure4.79e-14169
head8.79e-14123
ectoderm2.94e-13173
presumptive ectoderm2.94e-13173
regional part of cerebral cortex4.49e-1322
cerebral cortex5.67e-1225
pallium5.67e-1225
posterior neural tube1.18e-1115
chordal neural plate1.18e-1115
neocortex2.29e-1120
tube8.68e-11194
anatomical conduit1.06e-10241
nucleus of brain8.26e-109
neural nucleus8.26e-109
brainstem1.40e-098
basal ganglion2.00e-099
nuclear complex of neuraxis2.00e-099
aggregate regional part of brain2.00e-099
collection of basal ganglia2.00e-099
cerebral subcortex2.00e-099
anatomical cluster2.23e-09286
segmental subdivision of nervous system2.80e-0913
diencephalon2.31e-087
future diencephalon2.31e-087
segmental subdivision of hindbrain2.58e-0812
hindbrain2.58e-0812
presumptive hindbrain2.58e-0812
telencephalic nucleus5.76e-087
organ1.35e-07511
temporal lobe1.62e-077


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.