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Coexpression cluster:C2032: Difference between revisions

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|ontology_enrichment_disease=DOID:0060058!3.86e-11!10;DOID:2531!6.27e-07!51;DOID:0060083!6.27e-07!51
|ontology_enrichment_disease=DOID:0060058!3.86e-11!10;DOID:2531!6.27e-07!51;DOID:0060083!6.27e-07!51
|ontology_enrichment_uberon=UBERON:0007023!1.89e-16!115;UBERON:0001869!1.05e-09!32;UBERON:0002619!1.74e-09!22;UBERON:0001893!5.69e-09!34;UBERON:0001950!1.06e-08!20;UBERON:0000178!2.23e-08!15;UBERON:0000179!2.23e-08!15;UBERON:0000463!2.23e-08!15;UBERON:0002106!3.04e-08!3;UBERON:0004854!3.04e-08!3;UBERON:0009034!3.04e-08!3;UBERON:0002095!3.04e-08!3;UBERON:0004782!3.04e-08!3;UBERON:0003281!3.04e-08!3;UBERON:0009664!3.04e-08!3;UBERON:0002296!3.04e-08!3;UBERON:0005602!3.04e-08!3;UBERON:0001179!3.04e-08!3;UBERON:0006293!3.04e-08!3;UBERON:0000956!4.00e-08!25;UBERON:0000203!4.00e-08!25;UBERON:0002780!4.43e-08!41;UBERON:0001890!4.43e-08!41;UBERON:0006240!4.43e-08!41;UBERON:0002791!5.25e-08!33;UBERON:0003080!8.15e-08!42;UBERON:0002020!1.07e-07!34;UBERON:0003528!1.07e-07!34;UBERON:0001049!1.29e-07!57;UBERON:0005068!1.29e-07!57;UBERON:0006241!1.29e-07!57;UBERON:0007135!1.29e-07!57;UBERON:0001871!5.07e-07!7
|ontology_enrichment_uberon=UBERON:0007023!1.89e-16!115;UBERON:0001869!1.05e-09!32;UBERON:0002619!1.74e-09!22;UBERON:0001893!5.69e-09!34;UBERON:0001950!1.06e-08!20;UBERON:0000178!2.23e-08!15;UBERON:0000179!2.23e-08!15;UBERON:0000463!2.23e-08!15;UBERON:0002106!3.04e-08!3;UBERON:0004854!3.04e-08!3;UBERON:0009034!3.04e-08!3;UBERON:0002095!3.04e-08!3;UBERON:0004782!3.04e-08!3;UBERON:0003281!3.04e-08!3;UBERON:0009664!3.04e-08!3;UBERON:0002296!3.04e-08!3;UBERON:0005602!3.04e-08!3;UBERON:0001179!3.04e-08!3;UBERON:0006293!3.04e-08!3;UBERON:0000956!4.00e-08!25;UBERON:0000203!4.00e-08!25;UBERON:0002780!4.43e-08!41;UBERON:0001890!4.43e-08!41;UBERON:0006240!4.43e-08!41;UBERON:0002791!5.25e-08!33;UBERON:0003080!8.15e-08!42;UBERON:0002020!1.07e-07!34;UBERON:0003528!1.07e-07!34;UBERON:0001049!1.29e-07!57;UBERON:0005068!1.29e-07!57;UBERON:0006241!1.29e-07!57;UBERON:0007135!1.29e-07!57;UBERON:0001871!5.07e-07!7
|tf_chipseq_enrich=BATF#10538;3:18.2683513442277:0.000268166010572129:0.00286545835667512!BCL11A#53335;3:21.2770913277053:0.000170483911460614:0.00208028615831698!BCL3#602;2:17.2735514018692:0.00483449420807607:0.0226681216035403!BCLAF1#9774;2:10.8263238050609:0.0120220381643258:0.0436355614041851!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00365609373707621!MEF2A#4205;4:18.7432309096441:8.0978922767748e-06:0.000224095328959746!MEF2C#4208;2:20.655677246312:0.00340257057944504:0.0173533093440112!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434644806238105!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428051636741032!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172581812919079!REST#5978;3:7.23752153709602:0.00410469730419261:0.019565973608059!RXRA#6256;2:10.0373085695666:0.0139170380592011:0.0488663776850761!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.028086519665731!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162691581110376!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00975947712381512
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}}
}}

Revision as of 13:19, 5 September 2012


Full id: C2032_splenic_hairy_plasma_CD19_B_xeroderma_tonsil



Phase1 CAGE Peaks

Hg19::chr10:103649352..103649390,-p5@C10orf76
Hg19::chr21:16135576..16135586,-p@chr21:16135576..16135586
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Hg19::chr2:231454365..231454375,-p@chr2:231454365..231454375
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Hg19::chr2:231454377..231454382,-p@chr2:231454377..231454382
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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>

Uber Anatomy
Ontology termp-valuen
adult organism1.89e-16115
cerebral hemisphere1.05e-0932
regional part of cerebral cortex1.74e-0922
telencephalon5.69e-0934
neocortex1.06e-0820
blood2.23e-0815
haemolymphatic fluid2.23e-0815
organism substance2.23e-0815
spleen3.04e-083
gastrointestinal system mesentery3.04e-083
stomach region3.04e-083
mesentery3.04e-083
gastrointestinal system serosa3.04e-083
mesentery of stomach3.04e-083
gut mesentery3.04e-083
dorsal mesentery3.04e-083
dorsal mesogastrium3.04e-083
peritoneal cavity3.04e-083
spleen primordium3.04e-083
cerebral cortex4.00e-0825
pallium4.00e-0825
regional part of forebrain4.43e-0841
forebrain4.43e-0841
future forebrain4.43e-0841
regional part of telencephalon5.25e-0833
anterior neural tube8.15e-0842
gray matter1.07e-0734
brain grey matter1.07e-0734
neural tube1.29e-0757
neural rod1.29e-0757
future spinal cord1.29e-0757
neural keel1.29e-0757
temporal lobe5.07e-077
Disease
Ontology termp-valuen
lymphoma3.86e-1110
hematologic cancer6.27e-0751
immune system cancer6.27e-0751


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
BATF#10538318.26835134422770.0002681660105721290.00286545835667512
BCL11A#53335321.27709132770530.0001704839114606140.00208028615831698
BCL3#602217.27355140186920.004834494208076070.0226681216035403
BCLAF1#9774210.82632380506090.01202203816432580.0436355614041851
IRF4#3662316.43588451505810.0003669431395554610.00365609373707621
MEF2A#4205418.74323090964418.0978922767748e-060.000224095328959746
MEF2C#4208220.6556772463120.003402570579445040.0173533093440112
PAX5#507935.002174148383370.01196533174786410.0434644806238105
PBX3#5090210.95725634337210.01174530180688030.0428051636741032
RAD21#588537.766275421592250.0033411193858720.0172581812919079
REST#597837.237521537096020.004104697304192610.019565973608059
RXRA#6256210.03730856956660.01391703805920110.0488663776850761
SPI1#668836.153242631392040.006580387113059030.028086519665731
TCF12#693837.975848676639820.003090920396013070.0162691581110376
ZNF143#7702310.12565741417090.001534861610688180.00975947712381512



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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