Personal tools

Coexpression cluster:C1963

From FANTOM5_SSTAR

Revision as of 14:36, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1963_acute_CD14_Neutrophils_Dendritic_CD19_Eosinophils_CD34



Phase1 CAGE Peaks

Hg19::chr5:57787278..57787351,+p1@GAPT
Hg19::chrX:30595876..30595890,-p1@CXorf21
Hg19::chrX:30595907..30595941,-p2@CXorf21
Hg19::chrX:30595959..30595986,-p3@CXorf21
Hg19::chrX:30595997..30596014,-p5@CXorf21


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:0016491oxidoreductase activity0.0458024255269045



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 cell1.40e-85172
angioblastic mesenchymal cell1.40e-85172
hematopoietic oligopotent progenitor cell1.11e-80165
hematopoietic multipotent progenitor cell1.11e-80165
hematopoietic cell8.51e-80182
leukocyte2.61e-72140
hematopoietic lineage restricted progenitor cell2.83e-60124
myeloid cell2.26e-58112
common myeloid progenitor2.26e-58112
nongranular leukocyte2.15e-57119
myeloid leukocyte9.28e-4676
granulocyte monocyte progenitor cell2.94e-4171
myeloid lineage restricted progenitor cell5.50e-4070
macrophage dendritic cell progenitor1.12e-3765
monopoietic cell2.48e-3663
monocyte2.48e-3663
monoblast2.48e-3663
promonocyte2.48e-3663
CD14-positive, CD16-negative classical monocyte3.29e-3342
classical monocyte1.59e-2945
lymphocyte2.62e-1853
common lymphoid progenitor2.62e-1853
lymphoid lineage restricted progenitor cell9.69e-1852
lymphocyte of B lineage2.01e-1524
pro-B cell2.01e-1524
mesenchymal cell1.83e-13358
connective tissue cell2.79e-12365
B cell9.27e-1114
motile cell2.29e-08390
intermediate monocyte1.28e-079
CD14-positive, CD16-positive monocyte1.28e-079
granulocyte1.34e-078
dendritic cell1.64e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.87e-46102
blood island1.87e-46102
hemolymphoid system2.94e-41112
bone marrow7.95e-3680
bone element4.02e-3186
immune system2.87e-26115
adult organism6.05e-25115
skeletal element9.72e-23101
skeletal system9.72e-23101
connective tissue4.24e-11375
lateral plate mesoderm3.54e-09216
neural tube3.88e-0957
neural rod3.88e-0957
future spinal cord3.88e-0957
neural keel3.88e-0957
blood5.61e-0915
haemolymphatic fluid5.61e-0915
organism substance5.61e-0915
anterior neural tube8.12e-0842
regional part of forebrain1.03e-0741
forebrain1.03e-0741
future forebrain1.03e-0741
Disease
Ontology termp-valuen
hematologic cancer1.05e-1351
immune system cancer1.05e-1351
leukemia1.27e-1139
myeloid leukemia3.12e-1131


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
BCL11A#53335422.69556408288567.49488101632307e-060.00021451298395828
BCL3#602427.63768224299073.425174836939e-060.000114215145209155
EBF1#187947.12517347725520.0007230531046774210.00577419660493999
EP300#203345.419153380978560.00209386927943890.0121267461695403
IRF4#3662417.53161014939532.08739444052064e-050.0004610943062046
MEF2A#4205414.99458472771523.876195075647e-050.000728366206379087
NFKB1#479044.390450739355070.004707732692524960.0222093637489662
PAX5#507945.335652424942260.002223389586187790.0127825930304892
POU2F2#545247.284899246194020.0006631223288743860.00542714778663992
RFX5#599349.638328661756080.000221480125815720.00249850538561978
SP1#666744.558705102512720.00407573565781680.0194928679015766
SPI1#668846.563458806818180.0009957429636454020.00714443524183582
YY1#752843.928936599883080.007193866269917620.0298557599588288



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.