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Coexpression cluster:C2085: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!9.26e-86!114;UBERON:0001049!8.29e-34!56;UBERON:0005068!8.29e-34!56;UBERON:0006241!8.29e-34!56;UBERON:0007135!8.29e-34!56;UBERON:0000073!2.27e-29!53;UBERON:0002616!2.27e-29!53;UBERON:0003075!3.66e-27!82;UBERON:0007284!3.66e-27!82;UBERON:0002346!2.66e-25!86;UBERON:0001017!8.57e-25!81;UBERON:0010371!1.13e-22!104;UBERON:0001016!1.80e-22!89;UBERON:0002780!2.29e-22!41;UBERON:0001890!2.29e-22!41;UBERON:0003080!2.29e-22!41;UBERON:0006240!2.29e-22!41;UBERON:0000955!1.77e-21!68;UBERON:0006238!1.77e-21!68;UBERON:0010314!4.93e-21!132;UBERON:0003528!1.59e-17!34;UBERON:0002020!1.59e-17!34;UBERON:0001893!1.80e-17!34;UBERON:0011216!1.87e-17!223;UBERON:0004121!9.05e-16!171;UBERON:0000924!9.05e-16!171;UBERON:0006601!9.05e-16!171;UBERON:0002791!2.40e-15!32;UBERON:0003056!2.94e-15!61;UBERON:0001869!6.07e-15!32;UBERON:0003076!1.00e-12!15;UBERON:0003057!1.00e-12!15;UBERON:0000477!2.65e-11!373;UBERON:0002619!3.27e-11!22;UBERON:0000125!6.03e-11!9;UBERON:0002308!6.03e-11!9;UBERON:0000481!9.97e-11!342;UBERON:0002298!1.34e-10!6;UBERON:0004111!3.00e-10!240;UBERON:0000956!1.66e-09!25;UBERON:0000203!1.66e-09!25;UBERON:0004732!1.80e-09!13;UBERON:0001950!4.60e-09!20;UBERON:0000025!9.70e-09!192;UBERON:0009663!2.18e-08!7;UBERON:0002420!2.54e-08!9;UBERON:0007245!2.54e-08!9;UBERON:0010009!2.54e-08!9;UBERON:0010011!2.54e-08!9;UBERON:0000454!2.54e-08!9;UBERON:0004733!3.20e-08!12;UBERON:0002028!3.20e-08!12;UBERON:0007277!3.20e-08!12;UBERON:0002784!3.74e-08!4;UBERON:0000062!9.51e-08!503;UBERON:0002240!5.84e-07!3;UBERON:0005174!5.84e-07!3;UBERON:0001137!5.84e-07!3
|ontology_enrichment_uberon=UBERON:0007023!9.26e-86!114;UBERON:0001049!8.29e-34!56;UBERON:0005068!8.29e-34!56;UBERON:0006241!8.29e-34!56;UBERON:0007135!8.29e-34!56;UBERON:0000073!2.27e-29!53;UBERON:0002616!2.27e-29!53;UBERON:0003075!3.66e-27!82;UBERON:0007284!3.66e-27!82;UBERON:0002346!2.66e-25!86;UBERON:0001017!8.57e-25!81;UBERON:0010371!1.13e-22!104;UBERON:0001016!1.80e-22!89;UBERON:0002780!2.29e-22!41;UBERON:0001890!2.29e-22!41;UBERON:0003080!2.29e-22!41;UBERON:0006240!2.29e-22!41;UBERON:0000955!1.77e-21!68;UBERON:0006238!1.77e-21!68;UBERON:0010314!4.93e-21!132;UBERON:0003528!1.59e-17!34;UBERON:0002020!1.59e-17!34;UBERON:0001893!1.80e-17!34;UBERON:0011216!1.87e-17!223;UBERON:0004121!9.05e-16!171;UBERON:0000924!9.05e-16!171;UBERON:0006601!9.05e-16!171;UBERON:0002791!2.40e-15!32;UBERON:0003056!2.94e-15!61;UBERON:0001869!6.07e-15!32;UBERON:0003076!1.00e-12!15;UBERON:0003057!1.00e-12!15;UBERON:0000477!2.65e-11!373;UBERON:0002619!3.27e-11!22;UBERON:0000125!6.03e-11!9;UBERON:0002308!6.03e-11!9;UBERON:0000481!9.97e-11!342;UBERON:0002298!1.34e-10!6;UBERON:0004111!3.00e-10!240;UBERON:0000956!1.66e-09!25;UBERON:0000203!1.66e-09!25;UBERON:0004732!1.80e-09!13;UBERON:0001950!4.60e-09!20;UBERON:0000025!9.70e-09!192;UBERON:0009663!2.18e-08!7;UBERON:0002420!2.54e-08!9;UBERON:0007245!2.54e-08!9;UBERON:0010009!2.54e-08!9;UBERON:0010011!2.54e-08!9;UBERON:0000454!2.54e-08!9;UBERON:0004733!3.20e-08!12;UBERON:0002028!3.20e-08!12;UBERON:0007277!3.20e-08!12;UBERON:0002784!3.74e-08!4;UBERON:0000062!9.51e-08!503;UBERON:0002240!5.84e-07!3;UBERON:0005174!5.84e-07!3;UBERON:0001137!5.84e-07!3
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02,0.246177,0.0011123,0.0104945,0.000664446,0.0245539,0.0458843,0.122782,0.000223259,0.289049,0.0393151,0.125746,0.112897,0.0926658,0.000135709,0.205977,0.34423,0.0936726,0.343425,0.00917587,0.285122,0.22741,0.00166967,0.276721,0.00732664,0.264707,0.000388714
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}}
}}

Revision as of 15:17, 26 November 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
melanocyte5.79e-1210
melanoblast5.79e-1210
pigment cell5.25e-0814
light melanocyte3.76e-073
Uber Anatomy
Ontology termp-valuen
adult organism9.26e-86114
neural tube8.29e-3456
neural rod8.29e-3456
future spinal cord8.29e-3456
neural keel8.29e-3456
regional part of nervous system2.27e-2953
regional part of brain2.27e-2953
neural plate3.66e-2782
presumptive neural plate3.66e-2782
neurectoderm2.66e-2586
central nervous system8.57e-2581
ecto-epithelium1.13e-22104
nervous system1.80e-2289
regional part of forebrain2.29e-2241
forebrain2.29e-2241
anterior neural tube2.29e-2241
future forebrain2.29e-2241
brain1.77e-2168
future brain1.77e-2168
structure with developmental contribution from neural crest4.93e-21132
brain grey matter1.59e-1734
gray matter1.59e-1734
telencephalon1.80e-1734
organ system subdivision1.87e-17223
ectoderm-derived structure9.05e-16171
ectoderm9.05e-16171
presumptive ectoderm9.05e-16171
regional part of telencephalon2.40e-1532
pre-chordal neural plate2.94e-1561
cerebral hemisphere6.07e-1532
posterior neural tube1.00e-1215
chordal neural plate1.00e-1215
anatomical cluster2.65e-11373
regional part of cerebral cortex3.27e-1122
neural nucleus6.03e-119
nucleus of brain6.03e-119
multi-tissue structure9.97e-11342
brainstem1.34e-106
anatomical conduit3.00e-10240
cerebral cortex1.66e-0925
pallium1.66e-0925
segmental subdivision of nervous system1.80e-0913
neocortex4.60e-0920
tube9.70e-09192
telencephalic nucleus2.18e-087
basal ganglion2.54e-089
nuclear complex of neuraxis2.54e-089
aggregate regional part of brain2.54e-089
collection of basal ganglia2.54e-089
cerebral subcortex2.54e-089
segmental subdivision of hindbrain3.20e-0812
hindbrain3.20e-0812
presumptive hindbrain3.20e-0812
regional part of diencephalon3.74e-084
organ9.51e-08503
spinal cord5.84e-073
dorsal region element5.84e-073
dorsum5.84e-073


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.

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