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Coexpression cluster:C891: Difference between revisions

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|full_id=C891_Fibroblast_occipital_mesothelioma_cholangiocellular_neuroblastoma_pineal_hippocampus
|full_id=C891_Fibroblast_occipital_mesothelioma_cholangiocellular_neuroblastoma_pineal_hippocampus
|id=C891
|id=C891
|ontology_enrichment_celltype=CL:0000055!5.95e-09!180;CL:0002319!1.47e-07!25
|ontology_enrichment_celltype=CL:0002620!1.00e-11!23
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:17!2.19e-08!5;DOID:450!2.19e-08!5;DOID:66!2.19e-08!5;DOID:423!2.19e-08!5;DOID:0080000!2.19e-08!5;DOID:11722!2.19e-08!5
|ontology_enrichment_uberon=UBERON:0001017!2.15e-39!82;UBERON:0000073!6.98e-39!94;UBERON:0001016!6.98e-39!94;UBERON:0005743!2.66e-38!86;UBERON:0000955!6.54e-33!69;UBERON:0006238!6.54e-33!69;UBERON:0001049!1.16e-32!57;UBERON:0005068!1.16e-32!57;UBERON:0006241!1.16e-32!57;UBERON:0007135!1.16e-32!57;UBERON:0002616!3.27e-30!59;UBERON:0002346!1.27e-27!90;UBERON:0002780!6.47e-26!41;UBERON:0001890!6.47e-26!41;UBERON:0006240!6.47e-26!41;UBERON:0003075!7.91e-26!86;UBERON:0007284!7.91e-26!86;UBERON:0003080!8.33e-25!42;UBERON:0000924!1.30e-23!173;UBERON:0006601!1.30e-23!173;UBERON:0004121!4.89e-22!169;UBERON:0000033!5.05e-22!123;UBERON:0002020!5.34e-22!34;UBERON:0003528!5.34e-22!34;UBERON:0001893!6.35e-22!34;UBERON:0000153!9.41e-22!129;UBERON:0007811!9.41e-22!129;UBERON:0001869!1.14e-21!32;UBERON:0002791!3.51e-21!33;UBERON:0003056!4.27e-19!61;UBERON:0000475!1.09e-17!365;UBERON:0000956!2.44e-17!25;UBERON:0000203!2.44e-17!25;UBERON:0002619!3.96e-17!22;UBERON:0007023!5.13e-17!115;UBERON:0001950!1.58e-15!20;UBERON:0000468!1.61e-12!659;UBERON:0003076!6.38e-09!15;UBERON:0003057!6.38e-09!15;UBERON:0000481!7.36e-09!347;UBERON:0000467!1.47e-08!625;UBERON:0000025!1.67e-08!194;UBERON:0000480!2.01e-08!626;UBERON:0000483!1.22e-07!309;UBERON:0004733!1.43e-07!12;UBERON:0002028!1.43e-07!12;UBERON:0007277!1.43e-07!12;UBERON:0000922!1.93e-07!612;UBERON:0000119!2.15e-07!312
|ontology_enrichment_uberon=UBERON:0000073!6.67e-45!53;UBERON:0002616!6.67e-45!53;UBERON:0001049!2.98e-44!56;UBERON:0005068!2.98e-44!56;UBERON:0006241!2.98e-44!56;UBERON:0007135!2.98e-44!56;UBERON:0002780!3.42e-41!41;UBERON:0001890!3.42e-41!41;UBERON:0003080!3.42e-41!41;UBERON:0006240!3.42e-41!41;UBERON:0001017!8.97e-40!81;UBERON:0001869!1.38e-39!32;UBERON:0003528!2.84e-39!34;UBERON:0002020!2.84e-39!34;UBERON:0001893!3.54e-39!34;UBERON:0001016!4.98e-38!89;UBERON:0000955!1.13e-37!68;UBERON:0006238!1.13e-37!68;UBERON:0002619!2.17e-37!22;UBERON:0002791!1.67e-36!32;UBERON:0002346!2.04e-36!86;UBERON:0001950!7.99e-34!20;UBERON:0003075!1.35e-33!82;UBERON:0007284!1.35e-33!82;UBERON:0000956!3.52e-32!25;UBERON:0000203!3.52e-32!25;UBERON:0003056!6.93e-31!61;UBERON:0010371!1.05e-24!104;UBERON:0004121!4.79e-23!171;UBERON:0000924!4.79e-23!171;UBERON:0006601!4.79e-23!171;UBERON:0010314!1.06e-21!132;UBERON:0007023!5.22e-18!114;UBERON:0011216!6.66e-13!223;UBERON:0000200!7.99e-12!6;UBERON:0002021!1.56e-10!5;UBERON:0001871!4.81e-10!6;UBERON:0000349!5.01e-10!5;UBERON:0001872!5.69e-10!5;UBERON:0002420!4.50e-09!9;UBERON:0007245!4.50e-09!9;UBERON:0010009!4.50e-09!9;UBERON:0010011!4.50e-09!9;UBERON:0000454!4.50e-09!9;UBERON:0000062!4.61e-09!503;UBERON:0000025!6.79e-09!192;UBERON:0000125!1.14e-08!9;UBERON:0002308!1.14e-08!9;UBERON:0000369!9.10e-08!4;UBERON:0002435!9.10e-08!4;UBERON:0000204!9.10e-08!4;UBERON:0010082!9.10e-08!4;UBERON:0000064!3.92e-07!218;UBERON:0000477!4.07e-07!373;UBERON:0002298!6.95e-07!6
|tf_chipseq_enrich=CTCF#10664;6:3.57350424871668:0.00210388362937215:0.0121658547349537!TAF7#6879;4:5.08136417996618:0.0051419296120382:0.023905715222207
|tf_chipseq_enrich=CTCF#10664;6:3.57350424871668:0.00210388362937215:0.0121658547349537!TAF7#6879;4:5.08136417996618:0.0051419296120382:0.023905715222207
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}}
}}

Revision as of 16:50, 19 October 2012


Full id: C891_Fibroblast_occipital_mesothelioma_cholangiocellular_neuroblastoma_pineal_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:130303291..130303304,-p@chr12:130303291..130303304
-
Hg19::chr5:167000419..167000430,+p@chr5:167000419..167000430
+
Hg19::chr5:167000441..167000460,+p@chr5:167000441..167000460
+
Hg19::chr5:167000581..167000611,+p6@ODZ2
Hg19::chr5:167000625..167000675,+p5@ODZ2
Hg19::chr5:167000685..167000706,+p11@ODZ2
Hg19::chr5:167000707..167000719,+p16@ODZ2
Hg19::chr5:167000959..167001019,+p2@ODZ2
Hg19::chr5:167148342..167148357,+p1@ENST00000517346


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>


Cell Type
Ontology termp-valuen
skin fibroblast1.00e-1123
Uber Anatomy
Ontology termp-valuen
regional part of nervous system6.67e-4553
regional part of brain6.67e-4553
neural tube2.98e-4456
neural rod2.98e-4456
future spinal cord2.98e-4456
neural keel2.98e-4456
regional part of forebrain3.42e-4141
forebrain3.42e-4141
anterior neural tube3.42e-4141
future forebrain3.42e-4141
central nervous system8.97e-4081
cerebral hemisphere1.38e-3932
brain grey matter2.84e-3934
gray matter2.84e-3934
telencephalon3.54e-3934
nervous system4.98e-3889
brain1.13e-3768
future brain1.13e-3768
regional part of cerebral cortex2.17e-3722
regional part of telencephalon1.67e-3632
neurectoderm2.04e-3686
neocortex7.99e-3420
neural plate1.35e-3382
presumptive neural plate1.35e-3382
cerebral cortex3.52e-3225
pallium3.52e-3225
pre-chordal neural plate6.93e-3161
ecto-epithelium1.05e-24104
ectoderm-derived structure4.79e-23171
ectoderm4.79e-23171
presumptive ectoderm4.79e-23171
structure with developmental contribution from neural crest1.06e-21132
adult organism5.22e-18114
organ system subdivision6.66e-13223
gyrus7.99e-126
occipital lobe1.56e-105
temporal lobe4.81e-106
limbic system5.01e-105
parietal lobe5.69e-105
basal ganglion4.50e-099
nuclear complex of neuraxis4.50e-099
aggregate regional part of brain4.50e-099
collection of basal ganglia4.50e-099
cerebral subcortex4.50e-099
organ4.61e-09503
tube6.79e-09192
neural nucleus1.14e-089
nucleus of brain1.14e-089
corpus striatum9.10e-084
striatum9.10e-084
ventral part of telencephalon9.10e-084
future corpus striatum9.10e-084
organ part3.92e-07218
anatomical cluster4.07e-07373
brainstem6.95e-076
Disease
Ontology termp-valuen
musculoskeletal system disease2.19e-085
myotonic disease2.19e-085
muscle tissue disease2.19e-085
myopathy2.19e-085
muscular disease2.19e-085
myotonic dystrophy2.19e-085


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066463.573504248716680.002103883629372150.0121658547349537
TAF7#687945.081364179966180.00514192961203820.023905715222207



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.