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Coexpression cluster:C4176: Difference between revisions

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|full_id=C4176_Burkitt_Monocytederived_CD14_CD19_migratory_b_spleen
|full_id=C4176_Burkitt_Monocytederived_CD14_CD19_migratory_b_spleen
|id=C4176
|id=C4176
|ontology_enrichment_celltype=CL:0000738!1.72e-69!140;CL:0002087!1.13e-60!119;CL:0002031!1.37e-58!124;CL:0000037!6.41e-55!172;CL:0000566!6.41e-55!172;CL:0000988!3.24e-53!182;CL:0002032!2.94e-52!165;CL:0000837!2.94e-52!165;CL:0000766!3.49e-49!76;CL:0002009!3.19e-47!65;CL:0000557!3.58e-47!71;CL:0002194!9.83e-46!63;CL:0000576!9.83e-46!63;CL:0000040!9.83e-46!63;CL:0000559!9.83e-46!63;CL:0000839!1.09e-44!70;CL:0002057!2.85e-36!42;CL:0000763!5.24e-36!112;CL:0000049!5.24e-36!112;CL:0000860!9.44e-33!45;CL:0000945!9.70e-24!24;CL:0000826!9.70e-24!24;CL:0000542!6.11e-14!53;CL:0000051!6.11e-14!53;CL:0000236!7.35e-14!14;CL:0000838!2.86e-13!52;CL:0000134!2.88e-12!358;CL:0002320!2.09e-11!365;CL:0000990!5.26e-10!8;CL:0000451!3.34e-09!10;CL:0000219!1.74e-08!390;CL:0002393!3.17e-08!9;CL:0002397!3.17e-08!9;CL:0000840!8.57e-07!5;CL:0001029!8.57e-07!5
|ontology_enrichment_celltype=CL:0000738!5.09e-72!136;CL:0002087!2.19e-70!115;CL:0002031!1.14e-66!120;CL:0002009!7.97e-62!61;CL:0002194!5.35e-59!59;CL:0000576!5.35e-59!59;CL:0000040!5.35e-59!59;CL:0000559!5.35e-59!59;CL:0000557!4.01e-57!67;CL:0002032!5.69e-54!161;CL:0000837!5.69e-54!161;CL:0000037!8.57e-54!168;CL:0000566!8.57e-54!168;CL:0000839!2.57e-53!66;CL:0000988!9.43e-53!177;CL:0000766!4.45e-52!72;CL:0000473!7.96e-51!48;CL:0000234!7.96e-51!48;CL:0000860!3.19e-40!42;CL:0002057!3.19e-40!42;CL:0000763!1.33e-37!108;CL:0000049!1.33e-37!108;CL:0000945!2.80e-34!24;CL:0000826!2.80e-34!24;CL:0000325!2.98e-22!87;CL:0000236!1.87e-21!14;CL:0000990!6.01e-16!8;CL:0000542!4.10e-14!53;CL:0000051!4.10e-14!53;CL:0000134!1.43e-13!354;CL:0002242!2.44e-13!55;CL:0000838!2.78e-13!52;CL:0002320!6.77e-13!361;CL:0000451!1.20e-12!10;CL:0000235!1.33e-12!6;CL:0000840!7.87e-11!5;CL:0001029!7.87e-11!5;CL:0000219!1.50e-10!386;CL:0002393!1.94e-10!9;CL:0002397!1.94e-10!9;CL:0000453!1.95e-09!5;CL:0000048!8.99e-08!427;CL:0000723!2.12e-07!433;CL:0000034!2.24e-07!441;CL:0002619!4.37e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!3.66e-54!102;UBERON:0003061!3.66e-54!102;UBERON:0002193!5.69e-50!112;UBERON:0002371!3.14e-42!80;UBERON:0001474!1.37e-37!86;UBERON:0002405!1.78e-30!115;UBERON:0004765!1.69e-28!101;UBERON:0001434!1.69e-28!101;UBERON:0003081!2.25e-19!216;UBERON:0002204!1.49e-11!167;UBERON:0002384!1.18e-10!375;UBERON:0000178!2.59e-09!15;UBERON:0000179!2.59e-09!15;UBERON:0000463!2.59e-09!15
|ontology_enrichment_uberon=UBERON:0002390!1.21e-57!98;UBERON:0003061!1.21e-57!98;UBERON:0002193!1.28e-54!108;UBERON:0002405!9.35e-52!93;UBERON:0002371!1.31e-50!76;UBERON:0001474!9.85e-46!82;UBERON:0004765!3.03e-40!90;UBERON:0001434!1.25e-34!100;UBERON:0003081!4.07e-19!203;UBERON:0002204!2.03e-15!167;UBERON:0002384!1.59e-12!371;UBERON:0000926!3.91e-09!315;UBERON:0004120!3.91e-09!315;UBERON:0006603!3.91e-09!315
|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000778629253761237!EBF1#1879;3:8.906466846569:0.0014152328356098:0.0091702135574049!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270134850113408!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.017325744325423!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109241214389859
|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000778629253761237!EBF1#1879;3:8.906466846569:0.0014152328356098:0.0091702135574049!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270134850113408!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.017325744325423!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109241214389859
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}}
}}

Revision as of 15:44, 19 October 2012


Full id: C4176_Burkitt_Monocytederived_CD14_CD19_migratory_b_spleen



Phase1 CAGE Peaks

Hg19::chr2:208527094..208527114,+p1@ENST00000429730
Hg19::chr2:208527130..208527139,+p2@ENST00000429730
Hg19::chr2:208527157..208527162,+p3@ENST00000429730


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><br>


Cell Type
Ontology termp-valuen
leukocyte5.09e-72136
nongranular leukocyte2.19e-70115
hematopoietic lineage restricted progenitor cell1.14e-66120
macrophage dendritic cell progenitor7.97e-6261
monopoietic cell5.35e-5959
monocyte5.35e-5959
monoblast5.35e-5959
promonocyte5.35e-5959
granulocyte monocyte progenitor cell4.01e-5767
hematopoietic oligopotent progenitor cell5.69e-54161
hematopoietic multipotent progenitor cell5.69e-54161
hematopoietic stem cell8.57e-54168
angioblastic mesenchymal cell8.57e-54168
myeloid lineage restricted progenitor cell2.57e-5366
hematopoietic cell9.43e-53177
myeloid leukocyte4.45e-5272
defensive cell7.96e-5148
phagocyte7.96e-5148
classical monocyte3.19e-4042
CD14-positive, CD16-negative classical monocyte3.19e-4042
myeloid cell1.33e-37108
common myeloid progenitor1.33e-37108
lymphocyte of B lineage2.80e-3424
pro-B cell2.80e-3424
stuff accumulating cell2.98e-2287
B cell1.87e-2114
conventional dendritic cell6.01e-168
lymphocyte4.10e-1453
common lymphoid progenitor4.10e-1453
mesenchymal cell1.43e-13354
nucleate cell2.44e-1355
lymphoid lineage restricted progenitor cell2.78e-1352
connective tissue cell6.77e-13361
dendritic cell1.20e-1210
macrophage1.33e-126
immature conventional dendritic cell7.87e-115
common dendritic progenitor7.87e-115
motile cell1.50e-10386
intermediate monocyte1.94e-109
CD14-positive, CD16-positive monocyte1.94e-109
Langerhans cell1.95e-095
multi fate stem cell8.99e-08427
somatic stem cell2.12e-07433
stem cell2.24e-07441
adult endothelial progenitor cell4.37e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.21e-5798
blood island1.21e-5798
hemolymphoid system1.28e-54108
immune system9.35e-5293
bone marrow1.31e-5076
bone element9.85e-4682
skeletal element3.03e-4090
skeletal system1.25e-34100
lateral plate mesoderm4.07e-19203
musculoskeletal system2.03e-15167
connective tissue1.59e-12371
mesoderm3.91e-09315
mesoderm-derived structure3.91e-09315
presumptive mesoderm3.91e-09315


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#53335328.36945510360714.37778126761649e-050.000778629253761237
EBF1#187938.9064668465690.00141523283560980.0091702135574049
NFKB1#479035.488063424193840.006049381815655430.0270134850113408
PAX5#507936.669565531177830.003370290999677260.017325744325423
SPI1#668838.204323508522730.001810593189410520.0109241214389859



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.