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Coexpression cluster:C909: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!3.28e-10!51;DOID:0060083!3.28e-10!51;DOID:1240!3.39e-08!39
|ontology_enrichment_disease=DOID:2531!3.28e-10!51;DOID:0060083!3.28e-10!51;DOID:1240!3.39e-08!39
|ontology_enrichment_uberon=UBERON:0002390!1.62e-30!102;UBERON:0003061!1.62e-30!102;UBERON:0002193!1.21e-29!112;UBERON:0002371!1.61e-19!80;UBERON:0007023!1.16e-17!115;UBERON:0001474!3.67e-17!86;UBERON:0002405!5.70e-16!115;UBERON:0004765!8.50e-12!101;UBERON:0001434!8.50e-12!101;UBERON:0000178!2.60e-09!15;UBERON:0000179!2.60e-09!15;UBERON:0000463!2.60e-09!15
|ontology_enrichment_uberon=UBERON:0002390!1.62e-30!102;UBERON:0003061!1.62e-30!102;UBERON:0002193!1.21e-29!112;UBERON:0002371!1.61e-19!80;UBERON:0007023!1.16e-17!115;UBERON:0001474!3.67e-17!86;UBERON:0002405!5.70e-16!115;UBERON:0004765!8.50e-12!101;UBERON:0001434!8.50e-12!101;UBERON:0000178!2.60e-09!15;UBERON:0000179!2.60e-09!15;UBERON:0000463!2.60e-09!15
|tf_chipseq_enrich=CCNT2#905;5:3.52011198720146:0.00704556022641387:0.0293956241805065!EBF1#1879;4:3.95842970958622:0.01255739025408:0.0454161194288141!ELF1#1997;8:3.78497596338448:6.58614701323904e-05:0.00106726238621516!GABPB1#2553;6:4.71178922412145:0.000457630704900798:0.00421765735873054!MAX#4149;5:3.58475306055951:0.00650226248509667:0.0278429598885203!MYC#4609;7:4.06177478902954:0.000235555679657337:0.00256851113256762!NFKB1#4790;7:4.26849377437298:0.000169653664166286:0.00207306177978973!NFYA#4800;3:6.14186023327684:0.0104816316305809:0.0388188342505758!NFYB#4801;3:5.58659775117882:0.0135850027711194:0.0479520110995314!PAX5#5079;5:3.70531418398768:0.00561655707771942:0.0253934027982657!POLR2A#5430;8:1.90884726805162:0.011661228959883:0.0425849537166061!SMARCB1#6598;3:6.08423859371914:0.0107567140124601:0.0396982386214114!SP1#6667;5:3.1657674323005:0.0111972168609182:0.0411205081661604!SPI1#6688;5:4.55795750473485:0.00221269338710164:0.0127239007078245
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}}
}}

Revision as of 14:05, 5 September 2012


Full id: C909_Whole_CD19_CD8_Neutrophils_Eosinophils_CD4_blood



Phase1 CAGE Peaks

Hg19::chr15:40600231..40600255,+p@chr15:40600231..40600255
+
Hg19::chr17:29151686..29151766,-p1@CRLF3
Hg19::chr19:18391246..18391315,+p1@AB593186
Hg19::chr19:2290149..2290192,+p2@uc002lvo.1
Hg19::chr21:44204140..44204160,+p@chr21:44204140..44204160
+
Hg19::chr2:85822676..85822691,-p@chr2:85822676..85822691
-
Hg19::chr5:162932571..162932661,+p1@MAT2B
Hg19::chr5:176784837..176784936,+p1@RGS14
Hg19::chr6:32812568..32812631,+p2@PSMB9


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:0008831dTDP-4-dehydrorhamnose reductase activity0.00173083716001413
GO:0045226extracellular polysaccharide biosynthetic process0.00173083716001413
GO:0046379extracellular polysaccharide metabolic process0.00173083716001413
GO:0048269methionine adenosyltransferase complex0.00173083716001413
GO:0048270methionine adenosyltransferase regulator activity0.00173083716001413
GO:0006556S-adenosylmethionine biosynthetic process0.00288464368263519
GO:0046500S-adenosylmethionine metabolic process0.00370871841460287
GO:0000097sulfur amino acid biosynthetic process0.0216233659096436
GO:0000096sulfur amino acid metabolic process0.025928944303149
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.025928944303149
GO:0004298threonine endopeptidase activity0.025928944303149
GO:0033692cellular polysaccharide biosynthetic process0.025928944303149
GO:0000271polysaccharide biosynthetic process0.025928944303149
GO:0005839proteasome core complex (sensu Eukaryota)0.025928944303149
GO:0044272sulfur compound biosynthetic process0.025928944303149
GO:0000502proteasome complex (sensu Eukaryota)0.0369922818669568
GO:0044264cellular polysaccharide metabolic process0.0369922818669568
GO:0008652amino acid biosynthetic process0.0369922818669568
GO:0005976polysaccharide metabolic process0.0369922818669568
GO:0006790sulfur metabolic process0.0369922818669568
GO:0006575amino acid derivative metabolic process0.0369922818669568
GO:0043284biopolymer biosynthetic process0.0390134412752236
GO:0009968negative regulation of signal transduction0.0390134412752236
GO:0009309amine biosynthetic process0.0427614578009655
GO:0046483heterocycle metabolic process0.0448310930447899
GO:0016051carbohydrate biosynthetic process0.045748758593867
GO:0044271nitrogen compound biosynthetic process0.046045758423692
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.046045758423692
GO:0006730one-carbon compound metabolic process0.046045758423692
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0473686029795388
GO:0005057receptor signaling protein activity0.0491570475788475
GO:0006725aromatic compound metabolic process0.049226446731777



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 cell5.39e-65172
angioblastic mesenchymal cell5.39e-65172
hematopoietic oligopotent progenitor cell3.00e-61165
hematopoietic multipotent progenitor cell3.00e-61165
hematopoietic cell1.27e-59182
leukocyte1.03e-57140
hematopoietic lineage restricted progenitor cell1.23e-49124
nongranular leukocyte5.34e-48119
myeloid cell3.09e-33112
common myeloid progenitor3.09e-33112
myeloid leukocyte1.06e-2676
lymphocyte3.91e-2553
common lymphoid progenitor3.91e-2553
lymphoid lineage restricted progenitor cell6.14e-2552
granulocyte monocyte progenitor cell3.69e-2371
myeloid lineage restricted progenitor cell5.06e-2370
macrophage dendritic cell progenitor5.34e-2165
monopoietic cell1.83e-2063
monocyte1.83e-2063
monoblast1.83e-2063
promonocyte1.83e-2063
CD14-positive, CD16-negative classical monocyte1.48e-1742
classical monocyte5.23e-1745
T cell2.57e-1325
pro-T cell2.57e-1325
mature alpha-beta T cell1.13e-1118
alpha-beta T cell1.13e-1118
immature T cell1.13e-1118
mature T cell1.13e-1118
immature alpha-beta T cell1.13e-1118
lymphocyte of B lineage3.04e-1124
pro-B cell3.04e-1124
B cell1.08e-0814
CD8-positive, alpha-beta T cell4.68e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.62e-30102
blood island1.62e-30102
hemolymphoid system1.21e-29112
bone marrow1.61e-1980
adult organism1.16e-17115
bone element3.67e-1786
immune system5.70e-16115
skeletal element8.50e-12101
skeletal system8.50e-12101
blood2.60e-0915
haemolymphatic fluid2.60e-0915
organism substance2.60e-0915
Disease
Ontology termp-valuen
hematologic cancer3.28e-1051
immune system cancer3.28e-1051
leukemia3.39e-0839


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
CCNT2#90553.520111987201460.007045560226413870.0293956241805065
EBF1#187943.958429709586220.012557390254080.0454161194288141
ELF1#199783.784975963384486.58614701323904e-050.00106726238621516
GABPB1#255364.711789224121450.0004576307049007980.00421765735873054
MAX#414953.584753060559510.006502262485096670.0278429598885203
MYC#460974.061774789029540.0002355556796573370.00256851113256762
NFKB1#479074.268493774372980.0001696536641662860.00207306177978973
NFYA#480036.141860233276840.01048163163058090.0388188342505758
NFYB#480135.586597751178820.01358500277111940.0479520110995314
PAX5#507953.705314183987680.005616557077719420.0253934027982657
POLR2A#543081.908847268051620.0116612289598830.0425849537166061
SMARCB1#659836.084238593719140.01075671401246010.0396982386214114
SP1#666753.16576743230050.01119721686091820.0411205081661604
SPI1#668854.557957504734850.002212693387101640.0127239007078245



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.