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Coexpression cluster:C1055: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!4.40e-34!115;UBERON:0001049!8.72e-17!57;UBERON:0005068!8.72e-17!57;UBERON:0006241!8.72e-17!57;UBERON:0007135!8.72e-17!57;UBERON:0003080!2.86e-14!42;UBERON:0002780!4.86e-14!41;UBERON:0001890!4.86e-14!41;UBERON:0006240!4.86e-14!41;UBERON:0001017!6.42e-14!82;UBERON:0002390!3.27e-13!102;UBERON:0003061!3.27e-13!102;UBERON:0005743!3.89e-13!86;UBERON:0000073!6.24e-13!94;UBERON:0001016!6.24e-13!94;UBERON:0002616!1.13e-12!59;UBERON:0002193!2.54e-12!112;UBERON:0000955!1.13e-11!69;UBERON:0006238!1.13e-11!69;UBERON:0002020!1.55e-11!34;UBERON:0003528!1.55e-11!34;UBERON:0001893!1.92e-11!34;UBERON:0002791!3.47e-11!33;UBERON:0001869!1.30e-10!32;UBERON:0002346!5.00e-09!90;UBERON:0002619!1.17e-08!22;UBERON:0003075!1.89e-08!86;UBERON:0007284!1.89e-08!86;UBERON:0000956!3.58e-08!25;UBERON:0000203!3.58e-08!25;UBERON:0001950!4.25e-08!20;UBERON:0000178!6.90e-08!15;UBERON:0000179!6.90e-08!15;UBERON:0000463!6.90e-08!15
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}}
}}

Revision as of 16:49, 8 August 2012


Full id: C1055_CD19_thymus_CD4_CD8_Neutrophils_Natural_cerebellum



Phase1 CAGE Peaks

Hg19::chr17:8151353..8151381,-p1@CTC1
Hg19::chr1:204485503..204485555,+p1@MDM4
Hg19::chr2:206950781..206950947,-p1@INO80D
Hg19::chr4:76439596..76439643,-p2@RCHY1
Hg19::chr4:78741389..78741433,-p@chr4:78741389..78741433
-
Hg19::chr5:56469653..56469722,+p2@GPBP1
Hg19::chr7:21467642..21467671,+p2@SP4
Hg19::chr7:21467674..21467727,+p1@SP4


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:0045023G0 to G1 transition0.0105964942920282
GO:0000320re-entry into mitotic cell cycle0.0105964942920282
GO:0042177negative regulation of protein catabolic process0.0190677949582778
GO:0006357regulation of transcription from RNA polymerase II promoter0.0190677949582778
GO:0009895negative regulation of catabolic process0.0190677949582778
GO:0050821protein stabilization0.0233248915267865
GO:0042176regulation of protein catabolic process0.0233248915267865
GO:0006366transcription from RNA polymerase II promoter0.0233248915267865
GO:0031647regulation of protein stability0.0247044173842433
GO:0009894regulation of catabolic process0.026464343452305



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
leukocyte1.31e-35140
hematopoietic stem cell8.30e-35172
angioblastic mesenchymal cell8.30e-35172
hematopoietic oligopotent progenitor cell1.23e-31165
hematopoietic multipotent progenitor cell1.23e-31165
hematopoietic cell3.46e-31182
hematopoietic lineage restricted progenitor cell8.47e-28124
nongranular leukocyte4.37e-27119
lymphocyte1.56e-2153
common lymphoid progenitor1.56e-2153
lymphoid lineage restricted progenitor cell2.60e-2152
myeloid cell2.62e-12112
common myeloid progenitor2.62e-12112
mature alpha-beta T cell8.85e-1218
alpha-beta T cell8.85e-1218
immature T cell8.85e-1218
mature T cell8.85e-1218
immature alpha-beta T cell8.85e-1218
myeloid leukocyte3.36e-1176
T cell4.47e-1125
pro-T cell4.47e-1125
CD14-positive, CD16-negative classical monocyte5.79e-1042
lymphocyte of B lineage1.17e-0924
pro-B cell1.17e-0924
classical monocyte4.75e-0945
granulocyte monocyte progenitor cell8.31e-0971
B cell1.22e-0814
myeloid lineage restricted progenitor cell1.48e-0870
CD8-positive, alpha-beta T cell4.05e-0811
macrophage dendritic cell progenitor2.14e-0765
monopoietic cell5.58e-0763
monocyte5.58e-0763
monoblast5.58e-0763
promonocyte5.58e-0763
Uber Anatomy
Ontology termp-valuen
adult organism4.40e-34115
neural tube8.72e-1757
neural rod8.72e-1757
future spinal cord8.72e-1757
neural keel8.72e-1757
anterior neural tube2.86e-1442
regional part of forebrain4.86e-1441
forebrain4.86e-1441
future forebrain4.86e-1441
central nervous system6.42e-1482
hematopoietic system3.27e-13102
blood island3.27e-13102
regional part of nervous system6.24e-1394
nervous system6.24e-1394
regional part of brain1.13e-1259
hemolymphoid system2.54e-12112
brain1.13e-1169
future brain1.13e-1169
gray matter1.55e-1134
brain grey matter1.55e-1134
telencephalon1.92e-1134
regional part of telencephalon3.47e-1133
cerebral hemisphere1.30e-1032
neurectoderm5.00e-0990
regional part of cerebral cortex1.17e-0822
neural plate1.89e-0886
presumptive neural plate1.89e-0886
cerebral cortex3.58e-0825
pallium3.58e-0825
neocortex4.25e-0820
blood6.90e-0815
haemolymphatic fluid6.90e-0815
organism substance6.90e-0815


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)

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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.