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Coexpression cluster:C3457: Difference between revisions

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|full_id=C3457_Mast_cord_myeloma_CD4_plasma_b_CD14
|full_id=C3457_Mast_cord_myeloma_CD4_plasma_b_CD14
|id=C3457
|id=C3457
|ontology_enrichment_celltype=CL:0000037!3.69e-67!172;CL:0000566!3.69e-67!172;CL:0002032!3.54e-65!165;CL:0000837!3.54e-65!165;CL:0000988!5.40e-64!182;CL:0000738!6.74e-60!140;CL:0002031!1.16e-51!124;CL:0002087!1.58e-49!119;CL:0000763!2.23e-36!112;CL:0000049!2.23e-36!112;CL:0000766!2.76e-29!76;CL:0000557!3.23e-26!71;CL:0000542!2.08e-25!53;CL:0000051!2.08e-25!53;CL:0000839!5.96e-25!70;CL:0000838!8.36e-25!52;CL:0002009!1.92e-22!65;CL:0002194!5.70e-22!63;CL:0000576!5.70e-22!63;CL:0000040!5.70e-22!63;CL:0000559!5.70e-22!63;CL:0002057!1.10e-17!42;CL:0000860!7.36e-16!45;CL:0000084!3.09e-14!25;CL:0000827!3.09e-14!25;CL:0002320!5.31e-13!365;CL:0000134!7.77e-13!358;CL:0000791!2.02e-11!18;CL:0000789!2.02e-11!18;CL:0002420!2.02e-11!18;CL:0002419!2.02e-11!18;CL:0000790!2.02e-11!18;CL:0000945!2.07e-10!24;CL:0000826!2.07e-10!24;CL:0000219!2.47e-08!390;CL:0000625!1.43e-07!11
|ontology_enrichment_celltype=CL:0000037!1.53e-73!168;CL:0000566!1.53e-73!168;CL:0002032!1.28e-72!161;CL:0000837!1.28e-72!161;CL:0000988!5.19e-72!177;CL:0000738!6.27e-72!136;CL:0002031!8.69e-61!120;CL:0002087!2.47e-59!115;CL:0000763!1.53e-41!108;CL:0000049!1.53e-41!108;CL:0000766!4.92e-39!72;CL:0000557!1.38e-34!67;CL:0000839!1.38e-31!66;CL:0002009!1.00e-29!61;CL:0002194!6.11e-29!59;CL:0000576!6.11e-29!59;CL:0000040!6.11e-29!59;CL:0000559!6.11e-29!59;CL:0000542!5.65e-27!53;CL:0000051!5.65e-27!53;CL:0000838!3.19e-26!52;CL:0002242!3.15e-25!55;CL:0000473!3.54e-25!48;CL:0000234!3.54e-25!48;CL:0000860!4.33e-23!42;CL:0002057!4.33e-23!42;CL:0000084!1.73e-16!25;CL:0000827!1.73e-16!25;CL:0000791!1.31e-14!18;CL:0000789!1.31e-14!18;CL:0002420!1.31e-14!18;CL:0002419!1.31e-14!18;CL:0000790!1.31e-14!18;CL:0000134!4.49e-14!354;CL:0002320!5.48e-14!361;CL:0000219!1.40e-09!386;CL:0000625!1.47e-09!11;CL:0000945!1.95e-09!24;CL:0000826!1.95e-09!24;CL:0000325!1.97e-07!87;CL:0000094!7.20e-07!8
|ontology_enrichment_disease=DOID:2531!1.67e-13!51;DOID:0060083!1.67e-13!51;DOID:1240!9.61e-10!39;DOID:8692!2.08e-07!31
|ontology_enrichment_disease=DOID:2531!1.85e-10!51;DOID:0060083!1.85e-10!51;DOID:1240!7.75e-07!39
|ontology_enrichment_uberon=UBERON:0002390!1.62e-36!102;UBERON:0003061!1.62e-36!102;UBERON:0002193!1.78e-36!112;UBERON:0002371!4.75e-26!80;UBERON:0002405!7.60e-24!115;UBERON:0001474!1.69e-22!86;UBERON:0004765!2.10e-18!101;UBERON:0001434!2.10e-18!101;UBERON:0002384!1.65e-11!375;UBERON:0003081!3.26e-11!216;UBERON:0007023!6.06e-09!115;UBERON:0000178!4.99e-08!15;UBERON:0000179!4.99e-08!15;UBERON:0000463!4.99e-08!15
|ontology_enrichment_uberon=UBERON:0002390!3.96e-46!98;UBERON:0003061!3.96e-46!98;UBERON:0002193!1.82e-44!108;UBERON:0002405!4.31e-36!93;UBERON:0002371!3.31e-33!76;UBERON:0001474!7.50e-30!82;UBERON:0004765!2.89e-27!90;UBERON:0001434!1.58e-22!100;UBERON:0003081!1.68e-13!203;UBERON:0002384!8.70e-13!371;UBERON:0000178!6.70e-09!15;UBERON:0000179!6.70e-09!15;UBERON:0000463!6.70e-09!15
|tf_chipseq_enrich=BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183852156899741!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273786361031918!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00913846309621939!IRF4#3662;2:14.6096751244961:0.00605612247321789:0.0268176966283826!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324832210467934!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269133711371773!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0378065166898147
|tf_chipseq_enrich=BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183852156899741!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273786361031918!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00913846309621939!IRF4#3662;2:14.6096751244961:0.00605612247321789:0.0268176966283826!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324832210467934!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269133711371773!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0378065166898147
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}}
}}

Revision as of 15:07, 19 October 2012


Full id: C3457_Mast_cord_myeloma_CD4_plasma_b_CD14



Phase1 CAGE Peaks

Hg19::chr14:75988771..75988826,+p1@BATF
Hg19::chr14:75988831..75988847,+p2@BATF
Hg19::chr14:76005793..76005797,+p1@AY927507


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
hematopoietic stem cell1.53e-73168
angioblastic mesenchymal cell1.53e-73168
hematopoietic oligopotent progenitor cell1.28e-72161
hematopoietic multipotent progenitor cell1.28e-72161
hematopoietic cell5.19e-72177
leukocyte6.27e-72136
hematopoietic lineage restricted progenitor cell8.69e-61120
nongranular leukocyte2.47e-59115
myeloid cell1.53e-41108
common myeloid progenitor1.53e-41108
myeloid leukocyte4.92e-3972
granulocyte monocyte progenitor cell1.38e-3467
myeloid lineage restricted progenitor cell1.38e-3166
macrophage dendritic cell progenitor1.00e-2961
monopoietic cell6.11e-2959
monocyte6.11e-2959
monoblast6.11e-2959
promonocyte6.11e-2959
lymphocyte5.65e-2753
common lymphoid progenitor5.65e-2753
lymphoid lineage restricted progenitor cell3.19e-2652
nucleate cell3.15e-2555
defensive cell3.54e-2548
phagocyte3.54e-2548
classical monocyte4.33e-2342
CD14-positive, CD16-negative classical monocyte4.33e-2342
T cell1.73e-1625
pro-T cell1.73e-1625
mature alpha-beta T cell1.31e-1418
alpha-beta T cell1.31e-1418
immature T cell1.31e-1418
mature T cell1.31e-1418
immature alpha-beta T cell1.31e-1418
mesenchymal cell4.49e-14354
connective tissue cell5.48e-14361
motile cell1.40e-09386
CD8-positive, alpha-beta T cell1.47e-0911
lymphocyte of B lineage1.95e-0924
pro-B cell1.95e-0924
stuff accumulating cell1.97e-0787
granulocyte7.20e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.96e-4698
blood island3.96e-4698
hemolymphoid system1.82e-44108
immune system4.31e-3693
bone marrow3.31e-3376
bone element7.50e-3082
skeletal element2.89e-2790
skeletal system1.58e-22100
lateral plate mesoderm1.68e-13203
connective tissue8.70e-13371
blood6.70e-0915
haemolymphatic fluid6.70e-0915
organism substance6.70e-0915
Disease
Ontology termp-valuen
hematologic cancer1.85e-1051
immune system cancer1.85e-1051
leukemia7.75e-0739


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#53335218.91297006907140.003639406248379680.0183852156899741
BCLAF1#9774214.43509840674790.006201147435546130.0273786361031918
EBF1#187938.9064668465690.00141523283560980.00913846309621939
IRF4#3662214.60967512449610.006056122473217890.0268176966283826
MEF2A#4205212.4954872730960.008235029478029740.0324832210467934
NFKB1#479035.488063424193840.006049381815655430.0269133711371773
ZEB1#6935211.25895467836260.01010222676646330.0378065166898147



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.