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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1184_Natural_Basophils_blood_NK_Peripheral_Whole_CD8
|full_id=C1184_Natural_Basophils_blood_NK_Peripheral_Whole_CD8
|gostat_on_coexpression_clusters=GO:0042269!regulation of natural killer cell mediated cytotoxicity!0.00393951881941991!9437$GO:0016514!SWI/SNF complex!0.00393951881941991!9437$GO:0001910!regulation of leukocyte mediated cytotoxicity!0.00393951881941991!9437$GO:0031341!regulation of cell killing!0.00393951881941991!9437$GO:0042267!natural killer cell mediated cytotoxicity!0.00393951881941991!9437$GO:0002228!natural killer cell mediated immunity!0.00393951881941991!9437$GO:0001909!leukocyte mediated cytotoxicity!0.00429765689391263!9437$GO:0001906!cell killing!0.00429765689391263!9437$GO:0030101!natural killer cell activation!0.00429765689391263!9437$GO:0016585!chromatin remodeling complex!0.0088101966325209!9437$GO:0006968!cellular defense response!0.0128929706817379!9437$GO:0002449!lymphocyte mediated immunity!0.0128929706817379!9437$GO:0002443!leukocyte mediated immunity!0.0128929706817379!9437$GO:0002252!immune effector process!0.016331096196868!9437$GO:0045087!innate immune response!0.016331096196868!9437$GO:0046649!lymphocyte activation!0.0208167755798893!9437$GO:0005057!receptor signaling protein activity!0.0214882844695632!9437$GO:0045321!leukocyte activation!0.0214882844695632!9437$GO:0001775!cell activation!0.0217952599619855!9437$GO:0006917!induction of apoptosis!0.0217952599619855!9437$GO:0012502!induction of programmed cell death!0.0217952599619855!9437$GO:0043065!positive regulation of apoptosis!0.024104249535423!9437$GO:0043068!positive regulation of programmed cell death!0.024104249535423!9437$GO:0044451!nucleoplasm part!0.0404696024176773!9437$GO:0005654!nucleoplasm!0.0446096785588131!9437$GO:0042981!regulation of apoptosis!0.0448184218936603!9437$GO:0043067!regulation of programmed cell death!0.0448184218936603!9437$GO:0006952!defense response!0.0448184218936603!9437
|gostat_on_coexpression_clusters=GO:0042269!regulation of natural killer cell mediated cytotoxicity!0.00393951881941991!9437$GO:0016514!SWI/SNF complex!0.00393951881941991!9437$GO:0001910!regulation of leukocyte mediated cytotoxicity!0.00393951881941991!9437$GO:0031341!regulation of cell killing!0.00393951881941991!9437$GO:0042267!natural killer cell mediated cytotoxicity!0.00393951881941991!9437$GO:0002228!natural killer cell mediated immunity!0.00393951881941991!9437$GO:0001909!leukocyte mediated cytotoxicity!0.00429765689391263!9437$GO:0001906!cell killing!0.00429765689391263!9437$GO:0030101!natural killer cell activation!0.00429765689391263!9437$GO:0016585!chromatin remodeling complex!0.0088101966325209!9437$GO:0006968!cellular defense response!0.0128929706817379!9437$GO:0002449!lymphocyte mediated immunity!0.0128929706817379!9437$GO:0002443!leukocyte mediated immunity!0.0128929706817379!9437$GO:0002252!immune effector process!0.016331096196868!9437$GO:0045087!innate immune response!0.016331096196868!9437$GO:0046649!lymphocyte activation!0.0208167755798893!9437$GO:0005057!receptor signaling protein activity!0.0214882844695632!9437$GO:0045321!leukocyte activation!0.0214882844695632!9437$GO:0001775!cell activation!0.0217952599619855!9437$GO:0006917!induction of apoptosis!0.0217952599619855!9437$GO:0012502!induction of programmed cell death!0.0217952599619855!9437$GO:0043065!positive regulation of apoptosis!0.024104249535423!9437$GO:0043068!positive regulation of programmed cell death!0.024104249535423!9437$GO:0044451!nucleoplasm part!0.0404696024176773!9437$GO:0005654!nucleoplasm!0.0446096785588131!9437$GO:0042981!regulation of apoptosis!0.0448184218936603!9437$GO:0043067!regulation of programmed cell death!0.0448184218936603!9437$GO:0006952!defense response!0.0448184218936603!9437

Revision as of 13:40, 12 September 2012


Full id: C1184_Natural_Basophils_blood_NK_Peripheral_Whole_CD8



Phase1 CAGE Peaks

Hg19::chr12:9795420..9795436,+p@chr12:9795420..9795436
+
Hg19::chr12:9795452..9795469,+p@chr12:9795452..9795469
+
Hg19::chr14:22918081..22918089,+p1@TRDD3
Hg19::chr14:22918107..22918130,+p1@uc001wdw.2
Hg19::chr19:10226741..10226769,-p@chr19:10226741..10226769
-
Hg19::chr19:55417499..55417521,+p1@NCR1
Hg19::chr2:8464726..8464731,-p3@LINC00299


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


GO IDGO nameFDR corrected p-value
GO:0042269regulation of natural killer cell mediated cytotoxicity0.00393951881941991
GO:0016514SWI/SNF complex0.00393951881941991
GO:0001910regulation of leukocyte mediated cytotoxicity0.00393951881941991
GO:0031341regulation of cell killing0.00393951881941991
GO:0042267natural killer cell mediated cytotoxicity0.00393951881941991
GO:0002228natural killer cell mediated immunity0.00393951881941991
GO:0001909leukocyte mediated cytotoxicity0.00429765689391263
GO:0001906cell killing0.00429765689391263
GO:0030101natural killer cell activation0.00429765689391263
GO:0016585chromatin remodeling complex0.0088101966325209
GO:0006968cellular defense response0.0128929706817379
GO:0002449lymphocyte mediated immunity0.0128929706817379
GO:0002443leukocyte mediated immunity0.0128929706817379
GO:0002252immune effector process0.016331096196868
GO:0045087innate immune response0.016331096196868
GO:0046649lymphocyte activation0.0208167755798893
GO:0005057receptor signaling protein activity0.0214882844695632
GO:0045321leukocyte activation0.0214882844695632
GO:0001775cell activation0.0217952599619855
GO:0006917induction of apoptosis0.0217952599619855
GO:0012502induction of programmed cell death0.0217952599619855
GO:0043065positive regulation of apoptosis0.024104249535423
GO:0043068positive regulation of programmed cell death0.024104249535423
GO:0044451nucleoplasm part0.0404696024176773
GO:0005654nucleoplasm0.0446096785588131
GO:0042981regulation of apoptosis0.0448184218936603
GO:0043067regulation of programmed cell death0.0448184218936603
GO:0006952defense response0.0448184218936603



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
leukocyte1.58e-24140
hematopoietic stem cell3.80e-24172
angioblastic mesenchymal cell3.80e-24172
hematopoietic cell1.23e-23182
nongranular leukocyte1.84e-23119
hematopoietic oligopotent progenitor cell6.88e-22165
hematopoietic multipotent progenitor cell6.88e-22165
hematopoietic lineage restricted progenitor cell1.63e-20124
lymphoid lineage restricted progenitor cell8.95e-1852
lymphocyte5.34e-1753
common lymphoid progenitor5.34e-1753
mature alpha-beta T cell1.97e-1118
alpha-beta T cell1.97e-1118
immature T cell1.97e-1118
mature T cell1.97e-1118
immature alpha-beta T cell1.97e-1118
CD14-positive, CD16-negative classical monocyte5.48e-1142
T cell7.14e-1125
pro-T cell7.14e-1125
classical monocyte1.30e-0945
CD8-positive, alpha-beta T cell5.11e-0911
myeloid cell6.91e-08112
common myeloid progenitor6.91e-08112
B cell1.53e-0714
myeloid leukocyte1.60e-0776
monopoietic cell7.66e-0763
monocyte7.66e-0763
monoblast7.66e-0763
promonocyte7.66e-0763
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.13e-13102
blood island4.13e-13102
hemolymphoid system1.82e-12112
blood3.27e-1215
haemolymphatic fluid3.27e-1215
organism substance3.27e-1215


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.