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Coexpression cluster:C1070: Difference between revisions

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|full_id=C1070_hereditary_B_non_plasma_b_splenic_NK
|full_id=C1070_hereditary_B_non_plasma_b_splenic_NK
|id=C1070
|id=C1070
|ontology_enrichment_celltype=CL:0000542!1.90e-26!53;CL:0000051!1.90e-26!53;CL:0000838!4.10e-25!52;CL:0000945!6.51e-25!24;CL:0000826!6.51e-25!24;CL:0000037!2.79e-20!172;CL:0000566!2.79e-20!172;CL:0000988!3.54e-20!182;CL:0002032!1.09e-18!165;CL:0000837!1.09e-18!165;CL:0000738!4.79e-13!140;CL:0002087!7.99e-10!119;CL:0000236!1.22e-08!14;CL:0002031!2.50e-08!124;CL:0000817!1.83e-07!3;CL:0000084!8.48e-07!25;CL:0000827!8.48e-07!25
|ontology_enrichment_celltype=CL:0000945!2.61e-52!24;CL:0000826!2.61e-52!24;CL:0000838!2.16e-30!52;CL:0000542!8.16e-30!53;CL:0000051!8.16e-30!53;CL:0002242!1.01e-28!55;CL:0000946!5.16e-21!1;CL:0000786!5.16e-21!1;CL:0000980!5.16e-21!1;CL:0002127!7.72e-21!1;CL:0000914!7.72e-21!1;CL:0000911!7.72e-21!1;CL:0000814!7.72e-21!1;CL:0002042!7.72e-21!1;CL:0002039!7.72e-21!1;CL:0002040!7.72e-21!1;CL:0002041!7.72e-21!1;CL:0002087!1.92e-13!115;CL:0002031!7.18e-13!120;CL:0000738!2.58e-11!136;CL:0000785!3.35e-11!2;CL:0000955!3.35e-11!2;CL:0000818!3.35e-11!2;CL:0000954!3.35e-11!2;CL:0000816!3.35e-11!2;CL:0000893!4.09e-11!2;CL:0002489!4.09e-11!2;CL:0000809!4.09e-11!2;CL:0000808!4.09e-11!2;CL:0000894!4.09e-11!2;CL:0000806!4.09e-11!2;CL:0000807!4.09e-11!2;CL:0000805!4.09e-11!2;CL:0002425!4.09e-11!2;CL:0002032!1.71e-09!161;CL:0000837!1.71e-09!161;CL:0000037!4.45e-09!168;CL:0000566!4.45e-09!168;CL:0000988!1.36e-08!177;CL:0000817!6.78e-08!3
|ontology_enrichment_disease=DOID:2531!1.13e-32!51;DOID:0060083!1.13e-32!51;DOID:1240!5.82e-20!39;DOID:0060058!1.64e-18!10;DOID:8692!8.72e-12!31;DOID:0050686!2.91e-08!137
|ontology_enrichment_disease=DOID:2355!1.53e-21!1;DOID:630!6.31e-21!1;DOID:0050177!6.31e-21!1;DOID:0050427!6.31e-21!1;DOID:0060058!1.73e-18!10;DOID:74!1.82e-11!2
|ontology_enrichment_uberon=UBERON:0004177!6.19e-07!7;UBERON:0002106!9.23e-07!3;UBERON:0004854!9.23e-07!3;UBERON:0009034!9.23e-07!3;UBERON:0002095!9.23e-07!3;UBERON:0004782!9.23e-07!3;UBERON:0003281!9.23e-07!3;UBERON:0009664!9.23e-07!3;UBERON:0002296!9.23e-07!3;UBERON:0005602!9.23e-07!3;UBERON:0001179!9.23e-07!3;UBERON:0006293!9.23e-07!3
|ontology_enrichment_uberon=UBERON:0004177!3.15e-12!7;UBERON:0005057!3.15e-12!7;UBERON:0002106!6.34e-08!3;UBERON:0004854!6.34e-08!3;UBERON:0009034!6.34e-08!3;UBERON:0002095!6.34e-08!3;UBERON:0004782!6.34e-08!3;UBERON:0003281!6.34e-08!3;UBERON:0009664!6.34e-08!3;UBERON:0002296!6.34e-08!3;UBERON:0005602!6.34e-08!3;UBERON:0001179!6.34e-08!3;UBERON:0006293!6.34e-08!3
|tf_chipseq_enrich=MEF2A#4205;5:11.7145193185275:2.11059194855189e-05:0.000465430980816747!POU2F2#5452;4:4.55306202887126:0.00706247384683113:0.0294614837070297!SRF#6722;4:6.8985891310839:0.00152207190456878:0.00970059606036853
|tf_chipseq_enrich=MEF2A#4205;5:11.7145193185275:2.11059194855189e-05:0.000465430980816747!POU2F2#5452;4:4.55306202887126:0.00706247384683113:0.0294614837070297!SRF#6722;4:6.8985891310839:0.00152207190456878:0.00970059606036853
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}}
}}

Revision as of 10:47, 19 October 2012


Full id: C1070_hereditary_B_non_plasma_b_splenic_NK



Phase1 CAGE Peaks

Hg19::chr20:22201070..22201101,+p1@ENST00000439450
Hg19::chr2:106415317..106415347,-p@chr2:106415317..106415347
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Hg19::chr2:231524081..231524095,-p@chr2:231524081..231524095
-
Hg19::chr4:185275019..185275049,-p2@LOC728175
Hg19::chr4:185275051..185275071,-p5@LOC728175
Hg19::chr4:185275080..185275098,-p4@LOC728175
Hg19::chr7:31933122..31933152,-p@chr7:31933122..31933152
-
Hg19::chr8:21344644..21344671,-p@chr8:21344644..21344671
-


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
lymphocyte of B lineage2.61e-5224
pro-B cell2.61e-5224
lymphoid lineage restricted progenitor cell2.16e-3052
lymphocyte8.16e-3053
common lymphoid progenitor8.16e-3053
nucleate cell1.01e-2855
antibody secreting cell5.16e-211
plasma cell5.16e-211
plasmablast5.16e-211
innate effector T cell7.72e-211
immature NK T cell7.72e-211
effector T cell7.72e-211
mature NK T cell7.72e-211
immature NK T cell stage IV7.72e-211
immature NK T cell stage I7.72e-211
immature NK T cell stage II7.72e-211
immature NK T cell stage III7.72e-211
nongranular leukocyte1.92e-13115
hematopoietic lineage restricted progenitor cell7.18e-13120
leukocyte2.58e-11136
mature B cell3.35e-112
pre-B-II cell3.35e-112
transitional stage B cell3.35e-112
small pre-B-II cell3.35e-112
immature B cell3.35e-112
thymocyte4.09e-112
double negative thymocyte4.09e-112
double-positive, alpha-beta thymocyte4.09e-112
DN4 thymocyte4.09e-112
DN1 thymic pro-T cell4.09e-112
DN2 thymocyte4.09e-112
DN3 thymocyte4.09e-112
immature single positive thymocyte4.09e-112
early T lineage precursor4.09e-112
hematopoietic oligopotent progenitor cell1.71e-09161
hematopoietic multipotent progenitor cell1.71e-09161
hematopoietic stem cell4.45e-09168
angioblastic mesenchymal cell4.45e-09168
hematopoietic cell1.36e-08177
precursor B cell6.78e-083
Uber Anatomy
Ontology termp-valuen
hemopoietic organ3.15e-127
immune organ3.15e-127
spleen6.34e-083
gastrointestinal system mesentery6.34e-083
stomach region6.34e-083
mesentery6.34e-083
gastrointestinal system serosa6.34e-083
mesentery of stomach6.34e-083
gut mesentery6.34e-083
dorsal mesentery6.34e-083
dorsal mesogastrium6.34e-083
peritoneal cavity6.34e-083
spleen primordium6.34e-083
Disease
Ontology termp-valuen
anemia1.53e-211
genetic disease6.31e-211
monogenic disease6.31e-211
xeroderma pigmentosum6.31e-211
lymphoma1.73e-1810
hematopoietic system disease1.82e-112


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
MEF2A#4205511.71451931852752.11059194855189e-050.000465430980816747
POU2F2#545244.553062028871260.007062473846831130.0294614837070297
SRF#672246.89858913108390.001522071904568780.00970059606036853



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.