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Coexpression cluster:C1053: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0050794!regulation of cellular process!0.015938311957429!165631;60468;57492;124535;817$GO:0048096!chromatin-mediated maintenance of transcription!0.015938311957429!57492$GO:0005954!calcium- and calmodulin-dependent protein kinase complex!0.015938311957429!817$GO:0050789!regulation of biological process!0.015938311957429!165631;60468;57492;124535;817$GO:0006355!regulation of transcription, DNA-dependent!0.015938311957429!165631;60468;57492;124535$GO:0045815!positive regulation of gene expression, epigenetic!0.015938311957429!57492$GO:0006351!transcription, DNA-dependent!0.015938311957429!165631;60468;57492;124535$GO:0032774!RNA biosynthetic process!0.015938311957429!165631;60468;57492;124535$GO:0016514!SWI/SNF complex!0.015938311957429!57492$GO:0065007!biological regulation!0.015938311957429!165631;60468;57492;124535;817$GO:0045449!regulation of transcription!0.015938311957429!165631;60468;57492;124535$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.015938311957429!165631;60468;57492;124535$GO:0006350!transcription!0.015938311957429!165631;60468;57492;124535$GO:0010468!regulation of gene expression!0.015938311957429!165631;60468;57492;124535$GO:0031323!regulation of cellular metabolic process!0.0164057432460003!165631;60468;57492;124535$GO:0019222!regulation of metabolic process!0.0178265496741685!165631;60468;57492;124535$GO:0016070!RNA metabolic process!0.0178265496741685!165631;60468;57492;124535$GO:0043283!biopolymer metabolic process!0.0207611315204404!165631;60468;57492;124535;817$GO:0004683!calmodulin-dependent protein kinase activity!0.0216361309010111!817$GO:0003950!NAD+ ADP-ribosyltransferase activity!0.0371470414944187!165631$GO:0016585!chromatin remodeling complex!0.0381627203013111!57492$GO:0010467!gene expression!0.0381975373612162!165631;60468;57492;124535$GO:0043565!sequence-specific DNA binding!0.0444808009532835!60468;124535$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0453126974446688!165631;60468;57492;124535$GO:0006338!chromatin remodeling!0.0469739915798931!57492$GO:0005634!nucleus!0.0469739915798931!165631;60468;57492;124535$GO:0040029!regulation of gene expression, epigenetic!0.0469739915798931!57492
|gostat_on_coexpression_clusters=GO:0050794!regulation of cellular process!0.015938311957429!165631;60468;57492;124535;817$GO:0048096!chromatin-mediated maintenance of transcription!0.015938311957429!57492$GO:0005954!calcium- and calmodulin-dependent protein kinase complex!0.015938311957429!817$GO:0050789!regulation of biological process!0.015938311957429!165631;60468;57492;124535;817$GO:0006355!regulation of transcription, DNA-dependent!0.015938311957429!165631;60468;57492;124535$GO:0045815!positive regulation of gene expression, epigenetic!0.015938311957429!57492$GO:0006351!transcription, DNA-dependent!0.015938311957429!165631;60468;57492;124535$GO:0032774!RNA biosynthetic process!0.015938311957429!165631;60468;57492;124535$GO:0016514!SWI/SNF complex!0.015938311957429!57492$GO:0065007!biological regulation!0.015938311957429!165631;60468;57492;124535;817$GO:0045449!regulation of transcription!0.015938311957429!165631;60468;57492;124535$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.015938311957429!165631;60468;57492;124535$GO:0006350!transcription!0.015938311957429!165631;60468;57492;124535$GO:0010468!regulation of gene expression!0.015938311957429!165631;60468;57492;124535$GO:0031323!regulation of cellular metabolic process!0.0164057432460003!165631;60468;57492;124535$GO:0019222!regulation of metabolic process!0.0178265496741685!165631;60468;57492;124535$GO:0016070!RNA metabolic process!0.0178265496741685!165631;60468;57492;124535$GO:0043283!biopolymer metabolic process!0.0207611315204404!165631;60468;57492;124535;817$GO:0004683!calmodulin-dependent protein kinase activity!0.0216361309010111!817$GO:0003950!NAD+ ADP-ribosyltransferase activity!0.0371470414944187!165631$GO:0016585!chromatin remodeling complex!0.0381627203013111!57492$GO:0010467!gene expression!0.0381975373612162!165631;60468;57492;124535$GO:0043565!sequence-specific DNA binding!0.0444808009532835!60468;124535$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0453126974446688!165631;60468;57492;124535$GO:0006338!chromatin remodeling!0.0469739915798931!57492$GO:0005634!nucleus!0.0469739915798931!165631;60468;57492;124535$GO:0040029!regulation of gene expression, epigenetic!0.0469739915798931!57492
|id=C1053
|id=C1053
|ontology_enrichment_celltype=CL:0000738!1.98e-42!140;CL:0000037!7.81e-41!172;CL:0000566!7.81e-41!172;CL:0000988!4.50e-38!182;CL:0002032!5.32e-37!165;CL:0000837!5.32e-37!165;CL:0002031!7.36e-37!124;CL:0002087!3.85e-36!119;CL:0000542!1.12e-27!53;CL:0000051!1.12e-27!53;CL:0000838!3.94e-27!52;CL:0000945!2.55e-14!24;CL:0000826!2.55e-14!24;CL:0000763!6.28e-13!112;CL:0000049!6.28e-13!112;CL:0000557!2.44e-12!71;CL:0000766!3.44e-12!76;CL:0000084!3.91e-12!25;CL:0000827!3.91e-12!25;CL:0000791!9.19e-12!18;CL:0000789!9.19e-12!18;CL:0002420!9.19e-12!18;CL:0002419!9.19e-12!18;CL:0000790!9.19e-12!18;CL:0000839!1.23e-11!70;CL:0002057!5.46e-11!42;CL:0000236!2.41e-10!14;CL:0002009!4.52e-10!65;CL:0002194!1.21e-09!63;CL:0000576!1.21e-09!63;CL:0000040!1.21e-09!63;CL:0000559!1.21e-09!63;CL:0000860!1.48e-08!45;CL:0000625!7.89e-08!11
|ontology_enrichment_celltype=CL:0000738!1.52e-53!136;CL:0000037!8.01e-50!168;CL:0000566!8.01e-50!168;CL:0002087!1.07e-49!115;CL:0002031!1.33e-47!120;CL:0000988!3.91e-46!177;CL:0002032!1.24e-44!161;CL:0000837!1.24e-44!161;CL:0000542!7.45e-34!53;CL:0000051!7.45e-34!53;CL:0000838!4.14e-33!52;CL:0002242!9.22e-32!55;CL:0000945!7.45e-20!24;CL:0000826!7.45e-20!24;CL:0000557!8.08e-18!67;CL:0000766!6.11e-17!72;CL:0000839!3.17e-16!66;CL:0000791!3.08e-15!18;CL:0000789!3.08e-15!18;CL:0002420!3.08e-15!18;CL:0002419!3.08e-15!18;CL:0000790!3.08e-15!18;CL:0000763!5.66e-15!108;CL:0000049!5.66e-15!108;CL:0002194!7.78e-15!59;CL:0000576!7.78e-15!59;CL:0000040!7.78e-15!59;CL:0000559!7.78e-15!59;CL:0002009!1.03e-14!61;CL:0000236!1.03e-13!14;CL:0000860!8.84e-13!42;CL:0002057!8.84e-13!42;CL:0000084!2.61e-12!25;CL:0000827!2.61e-12!25;CL:0000473!7.67e-12!48;CL:0000234!7.67e-12!48;CL:0000625!4.30e-10!11;CL:0000134!4.32e-08!354;CL:0002320!1.74e-07!361;CL:0000624!7.29e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!2.62e-19!112;UBERON:0002390!1.19e-18!102;UBERON:0003061!1.19e-18!102;UBERON:0007023!3.78e-13!115;UBERON:0001474!3.73e-10!86;UBERON:0002371!5.58e-10!80;UBERON:0002405!7.69e-10!115;UBERON:0000178!1.26e-08!15;UBERON:0000179!1.26e-08!15;UBERON:0000463!1.26e-08!15;UBERON:0004765!1.36e-07!101;UBERON:0001434!1.36e-07!101
|ontology_enrichment_uberon=UBERON:0002193!2.19e-24!108;UBERON:0002390!1.18e-23!98;UBERON:0003061!1.18e-23!98;UBERON:0002405!1.39e-18!93;UBERON:0002371!3.13e-15!76;UBERON:0001474!7.62e-14!82;UBERON:0004765!1.79e-11!90;UBERON:0001434!5.73e-10!100;UBERON:0007023!7.49e-10!114;UBERON:0000178!3.56e-07!15;UBERON:0000179!3.56e-07!15;UBERON:0000463!3.56e-07!15
|tf_chipseq_enrich=BCLAF1#9774;4:10.8263238050609:0.000273875656269151:0.00292079032626303!NFKB1#4790;6:4.11604756814538:0.000729985658978431:0.00581621698489841!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127202903792869!TAF1#6872;7:2.92516550002713:0.00126532535791574:0.00849179508131102!YY1#7528;6:3.68337806239039:0.00136063115499274:0.00895700959321065
|tf_chipseq_enrich=BCLAF1#9774;4:10.8263238050609:0.000273875656269151:0.00292079032626303!NFKB1#4790;6:4.11604756814538:0.000729985658978431:0.00581621698489841!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127202903792869!TAF1#6872;7:2.92516550002713:0.00126532535791574:0.00849179508131102!YY1#7528;6:3.68337806239039:0.00136063115499274:0.00895700959321065
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}}
}}

Revision as of 10:45, 19 October 2012


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
leukocyte1.52e-53136
hematopoietic stem cell8.01e-50168
angioblastic mesenchymal cell8.01e-50168
nongranular leukocyte1.07e-49115
hematopoietic lineage restricted progenitor cell1.33e-47120
hematopoietic cell3.91e-46177
hematopoietic oligopotent progenitor cell1.24e-44161
hematopoietic multipotent progenitor cell1.24e-44161
lymphocyte7.45e-3453
common lymphoid progenitor7.45e-3453
lymphoid lineage restricted progenitor cell4.14e-3352
nucleate cell9.22e-3255
lymphocyte of B lineage7.45e-2024
pro-B cell7.45e-2024
granulocyte monocyte progenitor cell8.08e-1867
myeloid leukocyte6.11e-1772
myeloid lineage restricted progenitor cell3.17e-1666
mature alpha-beta T cell3.08e-1518
alpha-beta T cell3.08e-1518
immature T cell3.08e-1518
mature T cell3.08e-1518
immature alpha-beta T cell3.08e-1518
myeloid cell5.66e-15108
common myeloid progenitor5.66e-15108
monopoietic cell7.78e-1559
monocyte7.78e-1559
monoblast7.78e-1559
promonocyte7.78e-1559
macrophage dendritic cell progenitor1.03e-1461
B cell1.03e-1314
classical monocyte8.84e-1342
CD14-positive, CD16-negative classical monocyte8.84e-1342
T cell2.61e-1225
pro-T cell2.61e-1225
defensive cell7.67e-1248
phagocyte7.67e-1248
CD8-positive, alpha-beta T cell4.30e-1011
mesenchymal cell4.32e-08354
connective tissue cell1.74e-07361
CD4-positive, alpha-beta T cell7.29e-076
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.19e-24108
hematopoietic system1.18e-2398
blood island1.18e-2398
immune system1.39e-1893
bone marrow3.13e-1576
bone element7.62e-1482
skeletal element1.79e-1190
skeletal system5.73e-10100
adult organism7.49e-10114
blood3.56e-0715
haemolymphatic fluid3.56e-0715
organism substance3.56e-0715


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)

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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.