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Coexpression cluster:C250

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Full id: C250_Mast_Neutrophils_CD14_Eosinophils_CD8_Peripheral_CD4



Phase1 CAGE Peaks

  Short description
Hg19::chr10:3826687..3826699,- p@chr10:3826687..3826699
-
Hg19::chr16:27325702..27325750,- p@chr16:27325702..27325750
-
Hg19::chr16:27325969..27325994,+ p@chr16:27325969..27325994
+
Hg19::chr17:38506028..38506044,+ p@chr17:38506028..38506044
+
Hg19::chr19:13264446..13264492,+ p3@IER2
Hg19::chr19:13953130..13953158,- p@chr19:13953130..13953158
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Hg19::chr19:39897051..39897070,+ p3@ZFP36
Hg19::chr19:39898470..39898488,+ p@chr19:39898470..39898488
+
Hg19::chr19:39898498..39898514,+ p@chr19:39898498..39898514
+
Hg19::chr19:39898523..39898532,+ p@chr19:39898523..39898532
+
Hg19::chr19:39898544..39898598,+ p@chr19:39898544..39898598
+
Hg19::chr19:39898599..39898666,+ p@chr19:39898599..39898666
+
Hg19::chr19:39898678..39898692,- p@chr19:39898678..39898692
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Hg19::chr19:39898695..39898725,- p@chr19:39898695..39898725
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Hg19::chr19:39898701..39898712,+ p@chr19:39898701..39898712
+
Hg19::chr19:39898715..39898729,+ p@chr19:39898715..39898729
+
Hg19::chr19:39898746..39898756,+ p@chr19:39898746..39898756
+
Hg19::chr19:39898760..39898777,+ p@chr19:39898760..39898777
+
Hg19::chr19:39898772..39898888,- p1@CU679444
Hg19::chr19:39898781..39898796,+ p@chr19:39898781..39898796
+
Hg19::chr19:39898814..39898855,+ p@chr19:39898814..39898855
+
Hg19::chr19:39898896..39898901,+ p@chr19:39898896..39898901
+
Hg19::chr19:39898940..39898958,+ p@chr19:39898940..39898958
+
Hg19::chr19:39898968..39898980,+ p@chr19:39898968..39898980
+
Hg19::chr19:39898988..39899013,+ p@chr19:39898988..39899013
+
Hg19::chr19:39899024..39899036,+ p@chr19:39899024..39899036
+
Hg19::chr19:39899079..39899097,+ p@chr19:39899079..39899097
+
Hg19::chr19:39899258..39899276,+ p@chr19:39899258..39899276
+
Hg19::chr19:39899297..39899308,+ p@chr19:39899297..39899308
+
Hg19::chr19:39899540..39899551,+ p2@AJ227917
Hg19::chr19:39899566..39899574,- p8@CU679444
Hg19::chr19:39899597..39899634,+ p1@AJ227917
Hg19::chr19:39899887..39899894,+ p4@AJ227917
Hg19::chr1:204380074..204380108,- p8@PPP1R15B
Hg19::chr3:128445232..128445249,+ p@chr3:128445232..128445249
+
Hg19::chr3:39186740..39186774,- p@chr3:39186740..39186774
-
Hg19::chr3:39188204..39188217,- p3@CU691620
Hg19::chr5:172195219..172195236,- p3@AJ227912
Hg19::chr5:172195778..172195809,+ p@chr5:172195778..172195809
+
Hg19::chr5:172195833..172195881,- p2@AJ227912
Hg19::chr5:172195883..172195911,- p4@AJ227912
Hg19::chr5:172195926..172195937,- p13@AJ227912
Hg19::chr5:172195979..172196000,- p6@AJ227912
Hg19::chr5:172196072..172196092,- p5@AJ227912
Hg19::chr5:172196095..172196120,- p1@AJ227912
Hg19::chr5:172196608..172196676,- p@chr5:172196608..172196676
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Hg19::chr5:172196683..172196802,- p@chr5:172196683..172196802
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Hg19::chr5:172197180..172197212,- p2@AK127679
Hg19::chr5:172197219..172197279,- p1@AK127679
Hg19::chr5:172197282..172197310,- p3@AK127679
Hg19::chr6:35310813..35310823,+ p@chr6:35310813..35310823
+
Hg19::chr8:38645035..38645076,+ p11@TACC1


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:0017091AU-rich element binding0.00447427293064877
GO:0000289poly(A) tail shortening0.00447427293064877
GO:0050779RNA destabilization0.00447427293064877
GO:0000288mRNA catabolic process, deadenylation-dependent decay0.0134180779336029
GO:0043487regulation of RNA stability0.0134180779336029
GO:0043488regulation of mRNA stability0.0134180779336029
GO:0004726non-membrane spanning protein tyrosine phosphatase activity0.0134180779336029
GO:0031348negative regulation of defense response0.0134180779336029
GO:0050728negative regulation of inflammatory response0.0134180779336029
GO:0031124mRNA 3'-end processing0.0167644521049474
GO:0033549MAP kinase phosphatase activity0.0167644521049474
GO:0017017MAP kinase tyrosine/serine/threonine phosphatase activity0.0167644521049474
GO:0045638negative regulation of myeloid cell differentiation0.0167644521049474
GO:0031123RNA 3'-end processing0.0167644521049474
GO:0051252regulation of RNA metabolic process0.0167644521049474
GO:0003727single-stranded RNA binding0.0167644521049474
GO:0031347regulation of defense response0.0186230565034739
GO:0050727regulation of inflammatory response0.0186230565034739
GO:0006402mRNA catabolic process0.0201572588362358
GO:0007049cell cycle0.0201572588362358
GO:0045637regulation of myeloid cell differentiation0.0203953832529684
GO:0003729mRNA binding0.0203953832529684
GO:0048583regulation of response to stimulus0.0203953832529684
GO:0006401RNA catabolic process0.0256759940779331
GO:0006950response to stress0.032222988276366
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.032222988276366
GO:0045596negative regulation of cell differentiation0.032222988276366
GO:0030099myeloid cell differentiation0.035520473619963
GO:0051093negative regulation of developmental process0.035520473619963



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


Cell Type
Ontology termp-valuen
classical monocyte2.00e-3342
CD14-positive, CD16-negative classical monocyte2.00e-3342
defensive cell4.76e-2848
phagocyte4.76e-2848
myeloid leukocyte7.43e-2772
leukocyte1.71e-24136
granulocyte monocyte progenitor cell2.21e-2167
macrophage dendritic cell progenitor5.84e-2161
monopoietic cell1.31e-1959
monocyte1.31e-1959
monoblast1.31e-1959
promonocyte1.31e-1959
myeloid lineage restricted progenitor cell1.94e-1966
hematopoietic lineage restricted progenitor cell8.83e-17120
nongranular leukocyte1.35e-16115
stuff accumulating cell2.49e-1587
hematopoietic stem cell8.27e-14168
angioblastic mesenchymal cell8.27e-14168
myeloid cell3.72e-13108
common myeloid progenitor3.72e-13108
hematopoietic cell1.52e-12177
hematopoietic oligopotent progenitor cell2.21e-12161
hematopoietic multipotent progenitor cell2.21e-12161
granulocyte1.86e-088
intermediate monocyte3.71e-089
CD14-positive, CD16-positive monocyte3.71e-089
connective tissue cell7.17e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.95e-2598
blood island6.95e-2598
hemolymphoid system1.73e-22108
bone marrow4.07e-1976
immune system1.37e-1793
skeletal element1.55e-1790
bone element3.47e-1782
skeletal system8.22e-16100
adult organism1.31e-12114
lateral plate mesoderm3.05e-08203


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#905151.827750454893070.01240073781131270.0448930866330094
EBF1#1879233.939398797520911.8712595866431e-091.61915890612609e-07
HEY1#23462211.631583305869610.009367003429565320.0353514426039957
PAX5#5079202.565217511991473.10097941821131e-050.000628250610006927
POLR2A#5430502.064858823613539.85681600402904e-151.70719072412071e-12
USF2#7392266.49609869253487.30629970006958e-161.38486866492843e-13



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