Personal tools

Difference between revisions of "Coexpression cluster:C460"

From FANTOM5_SSTAR

Jump to: navigation, search
Line 3: Line 3:
 
|gostat_on_coexpression_clusters=GO:0004467!long-chain-fatty-acid-CoA ligase activity!0.0202658856665421!2180$GO:0015645!fatty-acid ligase activity!0.0202658856665421!2180$GO:0004000!adenosine deaminase activity!0.0202658856665421!105$GO:0003727!single-stranded RNA binding!0.0202658856665421!105$GO:0016877!ligase activity, forming carbon-sulfur bonds!0.0202658856665421!2180$GO:0019239!deaminase activity!0.0202658856665421!105$GO:0031903!microbody membrane!0.0202658856665421!2180$GO:0005778!peroxisomal membrane!0.0202658856665421!2180$GO:0044439!peroxisomal part!0.0202658856665421!2180$GO:0044438!microbody part!0.0202658856665421!2180$GO:0016814!hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines!0.0202658856665421!105$GO:0003725!double-stranded RNA binding!0.0202658856665421!105$GO:0005741!mitochondrial outer membrane!0.0254740322863236!2180$GO:0031968!organelle outer membrane!0.0254740322863236!2180$GO:0007586!digestion!0.0254740322863236!2180$GO:0019867!outer membrane!0.0254740322863236!2180$GO:0042579!microbody!0.0254740322863236!2180$GO:0005777!peroxisome!0.0254740322863236!2180$GO:0005792!microsome!0.0387065963269252!2180$GO:0042598!vesicular fraction!0.0387065963269252!2180$GO:0016810!hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds!0.0397555679538304!105$GO:0006631!fatty acid metabolic process!0.0397555679538304!2180
 
|gostat_on_coexpression_clusters=GO:0004467!long-chain-fatty-acid-CoA ligase activity!0.0202658856665421!2180$GO:0015645!fatty-acid ligase activity!0.0202658856665421!2180$GO:0004000!adenosine deaminase activity!0.0202658856665421!105$GO:0003727!single-stranded RNA binding!0.0202658856665421!105$GO:0016877!ligase activity, forming carbon-sulfur bonds!0.0202658856665421!2180$GO:0019239!deaminase activity!0.0202658856665421!105$GO:0031903!microbody membrane!0.0202658856665421!2180$GO:0005778!peroxisomal membrane!0.0202658856665421!2180$GO:0044439!peroxisomal part!0.0202658856665421!2180$GO:0044438!microbody part!0.0202658856665421!2180$GO:0016814!hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines!0.0202658856665421!105$GO:0003725!double-stranded RNA binding!0.0202658856665421!105$GO:0005741!mitochondrial outer membrane!0.0254740322863236!2180$GO:0031968!organelle outer membrane!0.0254740322863236!2180$GO:0007586!digestion!0.0254740322863236!2180$GO:0019867!outer membrane!0.0254740322863236!2180$GO:0042579!microbody!0.0254740322863236!2180$GO:0005777!peroxisome!0.0254740322863236!2180$GO:0005792!microsome!0.0387065963269252!2180$GO:0042598!vesicular fraction!0.0387065963269252!2180$GO:0016810!hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds!0.0397555679538304!105$GO:0006631!fatty acid metabolic process!0.0397555679538304!2180
 
|id=C460
 
|id=C460
 +
|ontology_enrichment_celltype=CL:0000037!1.36e-26!172;CL:0000566!1.36e-26!172;CL:0002032!7.02e-26!165;CL:0000837!7.02e-26!165;CL:0000988!6.57e-24!182;CL:0000738!8.69e-24!140;CL:0002087!1.91e-22!119;CL:0002031!2.95e-20!124;CL:0000542!7.30e-14!53;CL:0000051!7.30e-14!53;CL:0000838!1.70e-13!52;CL:0000763!1.51e-12!112;CL:0000049!1.51e-12!112;CL:0002057!1.74e-12!42;CL:0000860!1.35e-11!45;CL:0000766!2.79e-11!76;CL:0000084!1.20e-09!25;CL:0000827!1.20e-09!25;CL:0000839!5.02e-09!70;CL:0002194!1.90e-08!63;CL:0000576!1.90e-08!63;CL:0000040!1.90e-08!63;CL:0000559!1.90e-08!63;CL:0000791!1.03e-07!18;CL:0000789!1.03e-07!18;CL:0002420!1.03e-07!18;CL:0002419!1.03e-07!18;CL:0000790!1.03e-07!18;CL:0000557!1.19e-07!71;CL:0002009!1.60e-07!65
 +
|ontology_enrichment_disease=DOID:2531!1.31e-07!51;DOID:0060083!1.31e-07!51
 +
|ontology_enrichment_uberon=UBERON:0007023!1.90e-34!115;UBERON:0001049!7.58e-27!57;UBERON:0005068!7.58e-27!57;UBERON:0006241!7.58e-27!57;UBERON:0007135!7.58e-27!57;UBERON:0002780!4.59e-23!41;UBERON:0001890!4.59e-23!41;UBERON:0006240!4.59e-23!41;UBERON:0001017!2.16e-22!82;UBERON:0003080!8.59e-22!42;UBERON:0005743!8.94e-22!86;UBERON:0002616!3.08e-20!59;UBERON:0000073!4.97e-20!94;UBERON:0001016!4.97e-20!94;UBERON:0000955!6.81e-20!69;UBERON:0006238!6.81e-20!69;UBERON:0002020!4.12e-19!34;UBERON:0003528!4.12e-19!34;UBERON:0001893!4.72e-19!34;UBERON:0002791!1.78e-18!33;UBERON:0001869!1.18e-17!32;UBERON:0003075!5.59e-16!86;UBERON:0007284!5.59e-16!86;UBERON:0002346!1.53e-15!90;UBERON:0002619!6.15e-14!22;UBERON:0000956!1.67e-13!25;UBERON:0000203!1.67e-13!25;UBERON:0001950!1.12e-12!20;UBERON:0003056!3.29e-12!61;UBERON:0002390!2.38e-10!102;UBERON:0003061!2.38e-10!102;UBERON:0002193!1.10e-09!112;UBERON:0000153!3.88e-08!129;UBERON:0007811!3.88e-08!129;UBERON:0002308!3.67e-07!9;UBERON:0000125!3.67e-07!9;UBERON:0002420!4.53e-07!9;UBERON:0007245!4.53e-07!9;UBERON:0010009!4.53e-07!9;UBERON:0010011!4.53e-07!9;UBERON:0000454!4.53e-07!9;UBERON:0000033!5.18e-07!123
 
}}
 
}}

Revision as of 05:50, 21 May 2012


Full id: C460_Neutrophils_corpus_thalamus_substantia_parietal_globus_locus



Phase1 CAGE Peaks

  Short description
Hg19::chr10:1278750..1278767,- p@chr10:1278750..1278767
-
Hg19::chr10:1282470..1282519,- p3@ADARB2
Hg19::chr11:78049190..78049232,- p@chr11:78049190..78049232
-
Hg19::chr2:71804278..71804331,+ +
p@chr2:71804278..71804331
Hg19::chr4:185729602..185729613,- p15@ACSL1
Hg19::chr9:91985133..91985173,- p@chr9:91985133..91985173
-
Hg19::chr9:91985218..91985232,- p@chr9:91985218..91985232
-
Hg19::chr9:91985236..91985347,- p@chr9:91985236..91985347
-
Hg19::chr9:91985398..91985439,- p@chr9:91985398..91985439
-
Hg19::chr9:91985441..91985477,- p@chr9:91985441..91985477
-
Hg19::chr9:91985535..91985584,- p@chr9:91985535..91985584
-
Hg19::chr9:91985611..91985646,- p@chr9:91985611..91985646
-
Hg19::chr9:91985687..91985700,- p@chr9:91985687..91985700
-
Hg19::chr9:91985741..91985765,- p@chr9:91985741..91985765
-
Hg19::chr9:91985867..91985882,- p@chr9:91985867..91985882
-
Hg19::chr9:91985883..91985947,- p@chr9:91985883..91985947
-
Hg19::chr9:91986315..91986327,- p@chr9:91986315..91986327
-
Hg19::chr9:91987177..91987203,- p@chr9:91987177..91987203
-
Hg19::chr9:91987221..91987232,- p@chr9:91987221..91987232
-
Hg19::chr9:91987337..91987359,- p@chr9:91987337..91987359
-
Hg19::chr9:91987399..91987413,- p@chr9:91987399..91987413
-


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0202658856665421
GO:0015645fatty-acid ligase activity0.0202658856665421
GO:0004000adenosine deaminase activity0.0202658856665421
GO:0003727single-stranded RNA binding0.0202658856665421
GO:0016877ligase activity, forming carbon-sulfur bonds0.0202658856665421
GO:0019239deaminase activity0.0202658856665421
GO:0031903microbody membrane0.0202658856665421
GO:0005778peroxisomal membrane0.0202658856665421
GO:0044439peroxisomal part0.0202658856665421
GO:0044438microbody part0.0202658856665421
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0202658856665421
GO:0003725double-stranded RNA binding0.0202658856665421
GO:0005741mitochondrial outer membrane0.0254740322863236
GO:0031968organelle outer membrane0.0254740322863236
GO:0007586digestion0.0254740322863236
GO:0019867outer membrane0.0254740322863236
GO:0042579microbody0.0254740322863236
GO:0005777peroxisome0.0254740322863236
GO:0005792microsome0.0387065963269252
GO:0042598vesicular fraction0.0387065963269252
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0397555679538304
GO:0006631fatty acid metabolic process0.0397555679538304



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
hematopoietic stem cell1.36e-26172
angioblastic mesenchymal cell1.36e-26172
hematopoietic oligopotent progenitor cell7.02e-26165
hematopoietic multipotent progenitor cell7.02e-26165
hematopoietic cell6.57e-24182
leukocyte8.69e-24140
nongranular leukocyte1.91e-22119
hematopoietic lineage restricted progenitor cell2.95e-20124
lymphocyte7.30e-1453
common lymphoid progenitor7.30e-1453
lymphoid lineage restricted progenitor cell1.70e-1352
myeloid cell1.51e-12112
common myeloid progenitor1.51e-12112
CD14-positive, CD16-negative classical monocyte1.74e-1242
classical monocyte1.35e-1145
myeloid leukocyte2.79e-1176
T cell1.20e-0925
pro-T cell1.20e-0925
myeloid lineage restricted progenitor cell5.02e-0970
monopoietic cell1.90e-0863
monocyte1.90e-0863
monoblast1.90e-0863
promonocyte1.90e-0863
mature alpha-beta T cell1.03e-0718
alpha-beta T cell1.03e-0718
immature T cell1.03e-0718
mature T cell1.03e-0718
immature alpha-beta T cell1.03e-0718
granulocyte monocyte progenitor cell1.19e-0771
macrophage dendritic cell progenitor1.60e-0765
Uber Anatomy
Ontology termp-valuen
adult organism1.90e-34115
neural tube7.58e-2757
neural rod7.58e-2757
future spinal cord7.58e-2757
neural keel7.58e-2757
regional part of forebrain4.59e-2341
forebrain4.59e-2341
future forebrain4.59e-2341
central nervous system2.16e-2282
anterior neural tube8.59e-2242
regional part of brain3.08e-2059
regional part of nervous system4.97e-2094
nervous system4.97e-2094
brain6.81e-2069
future brain6.81e-2069
gray matter4.12e-1934
brain grey matter4.12e-1934
telencephalon4.72e-1934
regional part of telencephalon1.78e-1833
cerebral hemisphere1.18e-1732
neural plate5.59e-1686
presumptive neural plate5.59e-1686
neurectoderm1.53e-1590
regional part of cerebral cortex6.15e-1422
cerebral cortex1.67e-1325
pallium1.67e-1325
neocortex1.12e-1220
pre-chordal neural plate3.29e-1261
hematopoietic system2.38e-10102
blood island2.38e-10102
hemolymphoid system1.10e-09112
anterior region of body3.88e-08129
craniocervical region3.88e-08129
nucleus of brain3.67e-079
neural nucleus3.67e-079
basal ganglion4.53e-079
nuclear complex of neuraxis4.53e-079
aggregate regional part of brain4.53e-079
collection of basal ganglia4.53e-079
cerebral subcortex4.53e-079
head5.18e-07123
Disease
Ontology termp-valuen
hematologic cancer1.31e-0751
immune system cancer1.31e-0751


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.