Personal tools

Coexpression cluster:C1286

From FANTOM5_SSTAR

Revision as of 13:47, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1286_myelodysplastic_acute_leukemia_biphenotypic_CD14CD16_splenic_Dendritic



Phase1 CAGE Peaks

Hg19::chr8:130560794..130560810,-p@chr8:130560794..130560810
-
Hg19::chr8:130560812..130560823,-p@chr8:130560812..130560823
-
Hg19::chr8:130560843..130560854,-p@chr8:130560843..130560854
-
Hg19::chr8:130560902..130560915,-p@chr8:130560902..130560915
-
Hg19::chr8:130560925..130560948,-p@chr8:130560925..130560948
-
Hg19::chr8:130560949..130560959,-p@chr8:130560949..130560959
-
Hg19::chr8:27184282..27184305,+p6@PTK2B


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


No GOStat results

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
myeloid cell1.62e-46112
common myeloid progenitor1.62e-46112
hematopoietic stem cell2.79e-42172
angioblastic mesenchymal cell2.79e-42172
hematopoietic oligopotent progenitor cell3.60e-40165
hematopoietic multipotent progenitor cell3.60e-40165
hematopoietic cell1.78e-38182
CD14-positive, CD16-negative classical monocyte3.78e-3542
macrophage dendritic cell progenitor6.83e-3265
classical monocyte1.46e-3145
granulocyte monocyte progenitor cell3.81e-3171
monopoietic cell1.21e-3063
monocyte1.21e-3063
monoblast1.21e-3063
promonocyte1.21e-3063
myeloid leukocyte3.32e-3076
myeloid lineage restricted progenitor cell1.20e-2870
leukocyte4.95e-27140
nongranular leukocyte3.76e-25119
hematopoietic lineage restricted progenitor cell1.38e-23124
intermediate monocyte1.39e-099
CD14-positive, CD16-positive monocyte1.39e-099
mesenchymal cell1.68e-07358
connective tissue cell8.48e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.65e-35102
blood island6.65e-35102
hemolymphoid system3.64e-31112
bone marrow1.79e-2680
adult organism4.05e-24115
bone element4.43e-2386
immune system4.41e-21115
skeletal element4.67e-18101
skeletal system4.67e-18101
neural tube6.28e-1557
neural rod6.28e-1557
future spinal cord6.28e-1557
neural keel6.28e-1557
telencephalon2.15e-1434
regional part of forebrain3.49e-1441
forebrain3.49e-1441
future forebrain3.49e-1441
gray matter3.80e-1434
brain grey matter3.80e-1434
regional part of telencephalon8.30e-1433
anterior neural tube1.37e-1342
cerebral hemisphere2.78e-1332
regional part of brain4.52e-1259
regional part of cerebral cortex1.09e-1122
neocortex1.79e-1020
brain9.94e-1069
future brain9.94e-1069
cerebral cortex1.51e-0925
pallium1.51e-0925
central nervous system3.22e-0982
neural plate2.92e-0886
presumptive neural plate2.92e-0886
neurectoderm9.38e-0890
pre-chordal neural plate2.06e-0761
regional part of nervous system4.08e-0794
nervous system4.08e-0794
basal ganglion7.56e-079
nuclear complex of neuraxis7.56e-079
aggregate regional part of brain7.56e-079
collection of basal ganglia7.56e-079
cerebral subcortex7.56e-079
Disease
Ontology termp-valuen
myeloid leukemia3.08e-1731
leukemia2.07e-1539
hematologic cancer9.08e-1351
immune system cancer9.08e-1351


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
BATF#10538620.87811582197453.22775058778003e-082.17345611629374e-06
BCL11A#53335624.31667580309181.29931738009616e-089.61043965013196e-07
EBF1#187978.9064668465692.2473547136215e-071.19324595290247e-05
IRF4#3662412.52257867813950.0001356731131035550.00177719356069513
MEF2A#4205410.71041766265370.0002487360970091120.00268309742155904
NFKB1#479075.488063424193846.66568321176054e-060.000195002041723546
PAX5#507965.716770455295286.92762487228137e-050.00109956567482704
POU2F2#545267.805249192350731.11144903558223e-050.000284715785693336
RXRA#625638.603407345342830.003716461561497260.0187409361702097
SRF#6722611.82615279614389.50741412579311e-074.0677788770328e-05
USF1#739165.452713666178259.13505145927422e-050.00133173595666547
USF2#7392611.13616918720251.35815928956223e-065.33853210547948e-05
YY1#752864.209574928446160.000411683378865750.0039233324578301



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.