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Coexpression cluster:C1053

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Full id: C1053_CD19_CD4_Natural_CD8_Peripheral_granulocyte_tonsil



Phase1 CAGE Peaks

Hg19::chr17:56565257..56565283,-p2@HSF5
Hg19::chr3:122296443..122296454,+p3@PARP15
Hg19::chr3:122296465..122296476,+p2@PARP15
Hg19::chr3:122296477..122296503,+p1@PARP15
Hg19::chr4:114683412..114683431,-p10@CAMK2D
Hg19::chr6:157098579..157098634,+p4@ARID1B
Hg19::chr6:91006503..91006517,-p3@BACH2
Hg19::chr7:86848933..86848940,-p5@C7orf23


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:0050794regulation of cellular process0.015938311957429
GO:0048096chromatin-mediated maintenance of transcription0.015938311957429
GO:0005954calcium- and calmodulin-dependent protein kinase complex0.015938311957429
GO:0050789regulation of biological process0.015938311957429
GO:0006355regulation of transcription, DNA-dependent0.015938311957429
GO:0045815positive regulation of gene expression, epigenetic0.015938311957429
GO:0006351transcription, DNA-dependent0.015938311957429
GO:0032774RNA biosynthetic process0.015938311957429
GO:0016514SWI/SNF complex0.015938311957429
GO:0065007biological regulation0.015938311957429
GO:0045449regulation of transcription0.015938311957429
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.015938311957429
GO:0006350transcription0.015938311957429
GO:0010468regulation of gene expression0.015938311957429
GO:0031323regulation of cellular metabolic process0.0164057432460003
GO:0019222regulation of metabolic process0.0178265496741685
GO:0016070RNA metabolic process0.0178265496741685
GO:0043283biopolymer metabolic process0.0207611315204404
GO:0004683calmodulin-dependent protein kinase activity0.0216361309010111
GO:0003950NAD+ ADP-ribosyltransferase activity0.0371470414944187
GO:0016585chromatin remodeling complex0.0381627203013111
GO:0010467gene expression0.0381975373612162
GO:0043565sequence-specific DNA binding0.0444808009532835
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0453126974446688
GO:0006338chromatin remodeling0.0469739915798931
GO:0005634nucleus0.0469739915798931
GO:0040029regulation of gene expression, epigenetic0.0469739915798931



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><br>


Cell Type
Ontology termp-valuen
leukocyte1.98e-42140
hematopoietic stem cell7.81e-41172
angioblastic mesenchymal cell7.81e-41172
hematopoietic cell4.50e-38182
hematopoietic oligopotent progenitor cell5.32e-37165
hematopoietic multipotent progenitor cell5.32e-37165
hematopoietic lineage restricted progenitor cell7.36e-37124
nongranular leukocyte3.85e-36119
lymphocyte1.12e-2753
common lymphoid progenitor1.12e-2753
lymphoid lineage restricted progenitor cell3.94e-2752
lymphocyte of B lineage2.55e-1424
pro-B cell2.55e-1424
myeloid cell6.28e-13112
common myeloid progenitor6.28e-13112
granulocyte monocyte progenitor cell2.44e-1271
myeloid leukocyte3.44e-1276
T cell3.91e-1225
pro-T cell3.91e-1225
mature alpha-beta T cell9.19e-1218
alpha-beta T cell9.19e-1218
immature T cell9.19e-1218
mature T cell9.19e-1218
immature alpha-beta T cell9.19e-1218
myeloid lineage restricted progenitor cell1.23e-1170
CD14-positive, CD16-negative classical monocyte5.46e-1142
B cell2.41e-1014
macrophage dendritic cell progenitor4.52e-1065
monopoietic cell1.21e-0963
monocyte1.21e-0963
monoblast1.21e-0963
promonocyte1.21e-0963
classical monocyte1.48e-0845
CD8-positive, alpha-beta T cell7.89e-0811
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.62e-19112
hematopoietic system1.19e-18102
blood island1.19e-18102
adult organism3.78e-13115
bone element3.73e-1086
bone marrow5.58e-1080
immune system7.69e-10115
blood1.26e-0815
haemolymphatic fluid1.26e-0815
organism substance1.26e-0815
skeletal element1.36e-07101
skeletal system1.36e-07101


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
BCLAF1#9774410.82632380506090.0002738756562691510.00292079032626303
NFKB1#479064.116047568145380.0007299856589784310.00581621698489841
POLR2A#543082.147453176558070.002210725788971910.0127202903792869
TAF1#687272.925165500027130.001265325357915740.00849179508131102
YY1#752863.683378062390390.001360631154992740.00895700959321065



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.