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Coexpression cluster:C1638: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0031410574327759!3394;3665$GO:0045892!negative regulation of transcription, DNA-dependent!0.0031410574327759!3394;3665$GO:0045029!UDP-activated nucleotide receptor activity!0.0031410574327759!9934$GO:0003702!RNA polymerase II transcription factor activity!0.0031410574327759!3394;3665$GO:0016481!negative regulation of transcription!0.0031410574327759!3394;3665$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0031410574327759!3394;3665$GO:0015065!uridine nucleotide receptor activity!0.0031410574327759!9934$GO:0031324!negative regulation of cellular metabolic process!0.00387566435067731!3394;3665$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.00405724075135865!3394;3665$GO:0009892!negative regulation of metabolic process!0.00405724075135865!3394;3665$GO:0006366!transcription from RNA polymerase II promoter!0.00792110884661063!3394;3665$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.016104641718451!3394$GO:0048523!negative regulation of cellular process!0.016104641718451!3394;3665$GO:0003704!specific RNA polymerase II transcription factor activity!0.016104641718451!3665$GO:0048519!negative regulation of biological process!0.016104641718451!3394;3665$GO:0006955!immune response!0.016104641718451!3394;9934$GO:0001608!nucleotide receptor activity, G-protein coupled!0.016104641718451!9934$GO:0045028!purinergic nucleotide receptor activity, G-protein coupled!0.016104641718451!9934$GO:0016502!nucleotide receptor activity!0.016104641718451!9934$GO:0001614!purinergic nucleotide receptor activity!0.016104641718451!9934$GO:0002376!immune system process!0.0191868854807885!3394;9934$GO:0003700!transcription factor activity!0.0213752109800616!3394;3665$GO:0030099!myeloid cell differentiation!0.024483254351918!3394$GO:0009615!response to virus!0.0298436809913163!3665$GO:0030097!hemopoiesis!0.0469804302644277!3394$GO:0048534!hemopoietic or lymphoid organ development!0.0485232872745847!3394$GO:0002520!immune system development!0.0491439233431777!3394
|gostat_on_coexpression_clusters=GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0031410574327759!3394;3665$GO:0045892!negative regulation of transcription, DNA-dependent!0.0031410574327759!3394;3665$GO:0045029!UDP-activated nucleotide receptor activity!0.0031410574327759!9934$GO:0003702!RNA polymerase II transcription factor activity!0.0031410574327759!3394;3665$GO:0016481!negative regulation of transcription!0.0031410574327759!3394;3665$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0031410574327759!3394;3665$GO:0015065!uridine nucleotide receptor activity!0.0031410574327759!9934$GO:0031324!negative regulation of cellular metabolic process!0.00387566435067731!3394;3665$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.00405724075135865!3394;3665$GO:0009892!negative regulation of metabolic process!0.00405724075135865!3394;3665$GO:0006366!transcription from RNA polymerase II promoter!0.00792110884661063!3394;3665$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.016104641718451!3394$GO:0048523!negative regulation of cellular process!0.016104641718451!3394;3665$GO:0003704!specific RNA polymerase II transcription factor activity!0.016104641718451!3665$GO:0048519!negative regulation of biological process!0.016104641718451!3394;3665$GO:0006955!immune response!0.016104641718451!3394;9934$GO:0001608!nucleotide receptor activity, G-protein coupled!0.016104641718451!9934$GO:0045028!purinergic nucleotide receptor activity, G-protein coupled!0.016104641718451!9934$GO:0016502!nucleotide receptor activity!0.016104641718451!9934$GO:0001614!purinergic nucleotide receptor activity!0.016104641718451!9934$GO:0002376!immune system process!0.0191868854807885!3394;9934$GO:0003700!transcription factor activity!0.0213752109800616!3394;3665$GO:0030099!myeloid cell differentiation!0.024483254351918!3394$GO:0009615!response to virus!0.0298436809913163!3665$GO:0030097!hemopoiesis!0.0469804302644277!3394$GO:0048534!hemopoietic or lymphoid organ development!0.0485232872745847!3394$GO:0002520!immune system development!0.0491439233431777!3394
|id=C1638
|id=C1638
|ontology_enrichment_celltype=CL:0000738!1.57e-41!140;CL:0002087!6.76e-35!119;CL:0000037!1.13e-33!172;CL:0000566!1.13e-33!172;CL:0002031!2.45e-33!124;CL:0000988!7.53e-32!182;CL:0002032!1.12e-30!165;CL:0000837!1.12e-30!165;CL:0000766!5.84e-26!76;CL:0000557!1.66e-24!71;CL:0002057!2.55e-24!42;CL:0002009!6.61e-24!65;CL:0002194!1.23e-22!63;CL:0000576!1.23e-22!63;CL:0000040!1.23e-22!63;CL:0000559!1.23e-22!63;CL:0000839!3.28e-21!70;CL:0000860!6.12e-20!45;CL:0000763!6.89e-19!112;CL:0000049!6.89e-19!112;CL:0000542!4.80e-11!53;CL:0000051!4.80e-11!53;CL:0000838!6.84e-11!52;CL:0000945!7.85e-11!24;CL:0000826!7.85e-11!24;CL:0000236!3.01e-08!14
|ontology_enrichment_celltype=CL:0000738!9.16e-22!136;CL:0000037!5.72e-16!168;CL:0000566!5.72e-16!168;CL:0002031!1.50e-15!120;CL:0002087!1.81e-14!115;CL:0000988!6.11e-14!177;CL:0002032!2.62e-13!161;CL:0000837!2.62e-13!161;CL:0000766!3.79e-11!72;CL:0000557!1.21e-09!67;CL:0000236!2.65e-09!14;CL:0000838!9.69e-08!52;CL:0002009!1.06e-07!61;CL:0000542!1.92e-07!53;CL:0000051!1.92e-07!53;CL:0000839!1.97e-07!66;CL:0000860!5.03e-07!42;CL:0002057!5.03e-07!42;CL:0000763!6.77e-07!108;CL:0000049!6.77e-07!108;CL:0002242!6.94e-07!55
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.40e-30!115;UBERON:0002193!9.09e-29!112;UBERON:0002390!2.32e-28!102;UBERON:0003061!2.32e-28!102;UBERON:0002371!1.69e-20!80;UBERON:0002405!6.33e-19!115;UBERON:0001474!1.85e-17!86;UBERON:0004765!1.80e-12!101;UBERON:0001434!1.80e-12!101;UBERON:0001049!3.34e-09!57;UBERON:0005068!3.34e-09!57;UBERON:0006241!3.34e-09!57;UBERON:0007135!3.34e-09!57;UBERON:0003081!9.99e-09!216;UBERON:0003080!1.48e-07!42;UBERON:0002780!3.25e-07!41;UBERON:0001890!3.25e-07!41;UBERON:0006240!3.25e-07!41;UBERON:0002616!4.60e-07!59
|ontology_enrichment_uberon=UBERON:0007023!3.03e-61!114;UBERON:0001049!1.64e-15!56;UBERON:0005068!1.64e-15!56;UBERON:0006241!1.64e-15!56;UBERON:0007135!1.64e-15!56;UBERON:0002390!2.22e-14!98;UBERON:0003061!2.22e-14!98;UBERON:0000073!6.06e-14!53;UBERON:0002616!6.06e-14!53;UBERON:0002193!5.62e-13!108;UBERON:0002780!1.05e-11!41;UBERON:0001890!1.05e-11!41;UBERON:0003080!1.05e-11!41;UBERON:0006240!1.05e-11!41;UBERON:0003075!1.89e-10!82;UBERON:0007284!1.89e-10!82;UBERON:0003528!4.73e-10!34;UBERON:0002020!4.73e-10!34;UBERON:0001893!4.97e-10!34;UBERON:0002346!2.19e-09!86;UBERON:0001869!4.59e-09!32;UBERON:0002791!5.52e-09!32;UBERON:0000955!6.77e-09!68;UBERON:0006238!6.77e-09!68;UBERON:0001017!9.57e-09!81;UBERON:0002405!2.24e-08!93;UBERON:0002371!6.54e-08!76;UBERON:0000178!2.15e-07!15;UBERON:0000179!2.15e-07!15;UBERON:0000463!2.15e-07!15;UBERON:0001016!3.28e-07!89;UBERON:0000125!3.33e-07!9;UBERON:0002308!3.33e-07!9
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}}
}}

Revision as of 11:31, 19 October 2012


Full id: C1638_Dendritic_CD14_CD19_granulocyte_immature_acute_xeroderma



Phase1 CAGE Peaks

Hg19::chr11:615942..615957,-p1@IRF7
Hg19::chr16:85932760..85932775,+p1@IRF8
Hg19::chr3:150996176..150996198,-p5@P2RY14
Hg19::chr3:150996239..150996276,-p3@P2RY14
Hg19::chr3:150996322..150996336,-p2@P2RY14


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:0000122negative regulation of transcription from RNA polymerase II promoter0.0031410574327759
GO:0045892negative regulation of transcription, DNA-dependent0.0031410574327759
GO:0045029UDP-activated nucleotide receptor activity0.0031410574327759
GO:0003702RNA polymerase II transcription factor activity0.0031410574327759
GO:0016481negative regulation of transcription0.0031410574327759
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0031410574327759
GO:0015065uridine nucleotide receptor activity0.0031410574327759
GO:0031324negative regulation of cellular metabolic process0.00387566435067731
GO:0006357regulation of transcription from RNA polymerase II promoter0.00405724075135865
GO:0009892negative regulation of metabolic process0.00405724075135865
GO:0006366transcription from RNA polymerase II promoter0.00792110884661063
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.016104641718451
GO:0048523negative regulation of cellular process0.016104641718451
GO:0003704specific RNA polymerase II transcription factor activity0.016104641718451
GO:0048519negative regulation of biological process0.016104641718451
GO:0006955immune response0.016104641718451
GO:0001608nucleotide receptor activity, G-protein coupled0.016104641718451
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.016104641718451
GO:0016502nucleotide receptor activity0.016104641718451
GO:0001614purinergic nucleotide receptor activity0.016104641718451
GO:0002376immune system process0.0191868854807885
GO:0003700transcription factor activity0.0213752109800616
GO:0030099myeloid cell differentiation0.024483254351918
GO:0009615response to virus0.0298436809913163
GO:0030097hemopoiesis0.0469804302644277
GO:0048534hemopoietic or lymphoid organ development0.0485232872745847
GO:0002520immune system development0.0491439233431777



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
leukocyte9.16e-22136
hematopoietic stem cell5.72e-16168
angioblastic mesenchymal cell5.72e-16168
hematopoietic lineage restricted progenitor cell1.50e-15120
nongranular leukocyte1.81e-14115
hematopoietic cell6.11e-14177
hematopoietic oligopotent progenitor cell2.62e-13161
hematopoietic multipotent progenitor cell2.62e-13161
myeloid leukocyte3.79e-1172
granulocyte monocyte progenitor cell1.21e-0967
B cell2.65e-0914
lymphoid lineage restricted progenitor cell9.69e-0852
macrophage dendritic cell progenitor1.06e-0761
lymphocyte1.92e-0753
common lymphoid progenitor1.92e-0753
myeloid lineage restricted progenitor cell1.97e-0766
classical monocyte5.03e-0742
CD14-positive, CD16-negative classical monocyte5.03e-0742
myeloid cell6.77e-07108
common myeloid progenitor6.77e-07108
nucleate cell6.94e-0755
Uber Anatomy
Ontology termp-valuen
adult organism3.03e-61114
neural tube1.64e-1556
neural rod1.64e-1556
future spinal cord1.64e-1556
neural keel1.64e-1556
hematopoietic system2.22e-1498
blood island2.22e-1498
regional part of nervous system6.06e-1453
regional part of brain6.06e-1453
hemolymphoid system5.62e-13108
regional part of forebrain1.05e-1141
forebrain1.05e-1141
anterior neural tube1.05e-1141
future forebrain1.05e-1141
neural plate1.89e-1082
presumptive neural plate1.89e-1082
brain grey matter4.73e-1034
gray matter4.73e-1034
telencephalon4.97e-1034
neurectoderm2.19e-0986
cerebral hemisphere4.59e-0932
regional part of telencephalon5.52e-0932
brain6.77e-0968
future brain6.77e-0968
central nervous system9.57e-0981
immune system2.24e-0893
bone marrow6.54e-0876
blood2.15e-0715
haemolymphatic fluid2.15e-0715
organism substance2.15e-0715
nervous system3.28e-0789
neural nucleus3.33e-079
nucleus of brain3.33e-079


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.