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Coexpression cluster:C3184: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!8.12e-34!102;UBERON:0003061!8.12e-34!102;UBERON:0002193!2.38e-30!112;UBERON:0002371!2.02e-20!80;UBERON:0001474!1.59e-17!86;UBERON:0002405!7.82e-15!115;UBERON:0002384!2.47e-13!375;UBERON:0004765!5.21e-12!101;UBERON:0001434!5.21e-12!101;UBERON:0000178!2.95e-10!15;UBERON:0000179!2.95e-10!15;UBERON:0000463!2.95e-10!15
|ontology_enrichment_uberon=UBERON:0002390!8.12e-34!102;UBERON:0003061!8.12e-34!102;UBERON:0002193!2.38e-30!112;UBERON:0002371!2.02e-20!80;UBERON:0001474!1.59e-17!86;UBERON:0002405!7.82e-15!115;UBERON:0002384!2.47e-13!375;UBERON:0004765!5.21e-12!101;UBERON:0001434!5.21e-12!101;UBERON:0000178!2.95e-10!15;UBERON:0000179!2.95e-10!15;UBERON:0000463!2.95e-10!15
|pathway_enrichment=5.91277682223884e-05;0.0374278772847718;2;220;Signalling by NGF (Reactome):REACT_11061
|pathway_enrichment=5.91277682223884e-05;0.0374278772847718;2;220;Signalling by NGF (Reactome):REACT_11061
|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.0091260497726755!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460265034437471!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0377983900427277
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}}
}}

Revision as of 14:06, 5 September 2012


Full id: C3184_Eosinophils_CD8_CD4_Neutrophils_hairy_Whole_B



Phase1 CAGE Peaks

Hg19::chr11:64107589..64107604,-p@chr11:64107589..64107604
-
Hg19::chr19:6772686..6772697,+p2@VAV1
Hg19::chr22:24823517..24823546,+p5@ADORA2A


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


p.valueFDRnGenesnPathwayName
5.91277682223884e-050.03742787728477182220Signalling by NGF (Reactome):REACT_11061



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:0006909phagocytosis0.00025294983684129
GO:0010324membrane invagination0.00198514209351949
GO:0006897endocytosis0.00198514209351949
GO:0032230positive regulation of synaptic transmission, GABAergic0.00247927857153759
GO:0016044membrane organization and biogenesis0.00247927857153759
GO:0001973adenosine receptor signaling pathway0.00299401826913486
GO:0001611A2A adenosine receptor activity, G-protein coupled0.00299401826913486
GO:0032228regulation of synaptic transmission, GABAergic0.00349291848885374
GO:0042755eating behavior0.00349291848885374
GO:0051932synaptic transmission, GABAergic0.00349291848885374
GO:0001975response to amphetamine0.00349291848885374
GO:0014075response to amine stimulus0.00349291848885374
GO:0050790regulation of catalytic activity0.00366740246370577
GO:0016192vesicle-mediated transport0.00366740246370577
GO:0050806positive regulation of synaptic transmission0.00366740246370577
GO:0065009regulation of a molecular function0.00366740246370577
GO:0001609adenosine receptor activity, G-protein coupled0.00366740246370577
GO:0030676Rac guanyl-nucleotide exchange factor activity0.00366740246370577
GO:0051971positive regulation of transmission of nerve impulse0.00366740246370577
GO:0001963synaptic transmission, dopaminergic0.00366740246370577
GO:0031646positive regulation of neurological process0.00399167181551987
GO:0045785positive regulation of cell adhesion0.00714344921713767
GO:0050804regulation of synaptic transmission0.00728828147067584
GO:0051969regulation of transmission of nerve impulse0.00765586138917796
GO:0007270nerve-nerve synaptic transmission0.00765586138917796
GO:0006171cAMP biosynthetic process0.00765586138917796
GO:0046058cAMP metabolic process0.00851123181759712
GO:0007190adenylate cyclase activation0.00851123181759712
GO:0031644regulation of neurological process0.00851123181759712
GO:0045762positive regulation of adenylate cyclase activity0.00851123181759712
GO:0031281positive regulation of cyclase activity0.00851123181759712
GO:0051349positive regulation of lyase activity0.00851123181759712
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0109712805277906
GO:0007631feeding behavior0.0109712805277906
GO:0009190cyclic nucleotide biosynthetic process0.0109712805277906
GO:0045761regulation of adenylate cyclase activity0.0109712805277906
GO:0031279regulation of cyclase activity0.0109712805277906
GO:0051339regulation of lyase activity0.0109712805277906
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0109712805277906
GO:0001608nucleotide receptor activity, G-protein coupled0.0109712805277906
GO:0016502nucleotide receptor activity0.0109712805277906
GO:0001614purinergic nucleotide receptor activity0.0109712805277906
GO:0009187cyclic nucleotide metabolic process0.0121763494559456
GO:0007242intracellular signaling cascade0.0135282592478952
GO:0019992diacylglycerol binding0.0137276904705138
GO:0010033response to organic substance0.0141114826117002
GO:0030155regulation of cell adhesion0.0147014195766507
GO:0006968cellular defense response0.0157024009538919
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0175506373098121
GO:0007229integrin-mediated signaling pathway0.0175506373098121
GO:0019933cAMP-mediated signaling0.0175506373098121
GO:0007166cell surface receptor linked signal transduction0.0175506373098121
GO:0007596blood coagulation0.0197432993336674
GO:0050817coagulation0.019764653657151
GO:0007599hemostasis0.0199751569658774
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0218567002300837
GO:0019935cyclic-nucleotide-mediated signaling0.0223892589633975
GO:0050878regulation of body fluid levels0.0225433032418296
GO:0042060wound healing0.0232228968375412
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0262997025568311
GO:0016043cellular component organization and biogenesis0.0262997025568311
GO:0008015blood circulation0.0262997025568311
GO:0003013circulatory system process0.0262997025568311
GO:0035023regulation of Rho protein signal transduction0.0262997025568311
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0265368819590599
GO:0007626locomotory behavior0.0286623246375753
GO:0007266Rho protein signal transduction0.0293234423434123
GO:0043087regulation of GTPase activity0.0324158935762655
GO:0007417central nervous system development0.0355671701565904
GO:0006810transport0.0358650919401976
GO:0051234establishment of localization0.0366111125560204
GO:0009165nucleotide biosynthetic process0.0366111125560204
GO:0043085positive regulation of catalytic activity0.0366111125560204
GO:0019932second-messenger-mediated signaling0.0378026194446836
GO:0051239regulation of multicellular organismal process0.0385460220629078
GO:0007268synaptic transmission0.039193714268358
GO:0006954inflammatory response0.039193714268358
GO:0007610behavior0.039193714268358
GO:0051179localization0.039193714268358
GO:0051336regulation of hydrolase activity0.0397950531681832
GO:0005085guanyl-nucleotide exchange factor activity0.0397950531681832
GO:0019226transmission of nerve impulse0.0419682489221858
GO:0009117nucleotide metabolic process0.0427127318453849
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0455375661295008
GO:0046578regulation of Ras protein signal transduction0.0458554250684929
GO:0007165signal transduction0.0474101992469932



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
hematopoietic stem cell4.21e-90172
angioblastic mesenchymal cell4.21e-90172
hematopoietic cell3.34e-86182
hematopoietic oligopotent progenitor cell3.46e-84165
hematopoietic multipotent progenitor cell3.46e-84165
leukocyte8.98e-79140
nongranular leukocyte5.90e-64119
hematopoietic lineage restricted progenitor cell3.06e-63124
lymphocyte5.64e-4253
common lymphoid progenitor5.64e-4253
lymphoid lineage restricted progenitor cell2.00e-4152
myeloid cell1.90e-39112
common myeloid progenitor1.90e-39112
myeloid leukocyte6.85e-2876
granulocyte monocyte progenitor cell1.85e-2371
myeloid lineage restricted progenitor cell9.51e-2270
macrophage dendritic cell progenitor2.07e-2165
T cell5.49e-2125
pro-T cell5.49e-2125
monopoietic cell1.61e-2063
monocyte1.61e-2063
monoblast1.61e-2063
promonocyte1.61e-2063
lymphocyte of B lineage7.38e-1924
pro-B cell7.38e-1924
CD14-positive, CD16-negative classical monocyte4.90e-1842
mature alpha-beta T cell3.73e-1618
alpha-beta T cell3.73e-1618
immature T cell3.73e-1618
mature T cell3.73e-1618
immature alpha-beta T cell3.73e-1618
classical monocyte6.76e-1645
mesenchymal cell2.24e-15358
connective tissue cell3.33e-14365
motile cell7.04e-12390
B cell4.85e-1114
CD8-positive, alpha-beta T cell6.40e-1111
granulocyte9.72e-088
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.12e-34102
blood island8.12e-34102
hemolymphoid system2.38e-30112
bone marrow2.02e-2080
bone element1.59e-1786
immune system7.82e-15115
connective tissue2.47e-13375
skeletal element5.21e-12101
skeletal system5.21e-12101
blood2.95e-1015
haemolymphatic fluid2.95e-1015
organism substance2.95e-1015
Disease
Ontology termp-valuen
hematologic cancer4.28e-2051
immune system cancer4.28e-2051
leukemia2.56e-1539
myeloid leukemia3.33e-1031
lymphoma3.20e-0810


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
EBF1#187938.9064668465690.00141523283560980.0091260497726755
ELF1#199734.258097958807540.01295179875054610.0460265034437471
ZEB1#6935211.25895467836260.01010222676646330.0377983900427277



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.