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{{Coexpression_clusters
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|full_id=C752_CD4_acute_NK_chronic_CD14_Neutrophils_lymphoma
|id=C752
|ontology_enrichment_celltype=CL:0000738!5.30e-31!140;CL:0002031!3.01e-29!124;CL:0002087!1.10e-28!119;CL:0000037!1.48e-26!172;CL:0000566!1.48e-26!172;CL:0002032!7.03e-25!165;CL:0000837!7.03e-25!165;CL:0000988!8.59e-24!182;CL:0000766!2.68e-22!76;CL:0002057!3.23e-22!42;CL:0000557!6.28e-22!71;CL:0000839!2.90e-21!70;CL:0000860!4.71e-20!45;CL:0002009!8.53e-20!65;CL:0002194!1.25e-19!63;CL:0000576!1.25e-19!63;CL:0000040!1.25e-19!63;CL:0000559!1.25e-19!63;CL:0000763!1.90e-16!112;CL:0000049!1.90e-16!112;CL:0000838!1.90e-08!52;CL:0000542!3.64e-08!53;CL:0000051!3.64e-08!53;CL:0000134!2.49e-07!358;CL:0002393!5.94e-07!9;CL:0002397!5.94e-07!9;CL:0002320!8.46e-07!365
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002371!2.74e-19!80;UBERON:0001474!6.18e-18!86;UBERON:0002390!8.51e-18!102;UBERON:0003061!8.51e-18!102;UBERON:0002193!1.15e-15!112;UBERON:0004765!4.11e-14!101;UBERON:0001434!4.11e-14!101;UBERON:0002405!1.05e-12!115;UBERON:0001049!1.38e-08!57;UBERON:0005068!1.38e-08!57;UBERON:0006241!1.38e-08!57;UBERON:0007135!1.38e-08!57
}}

Latest revision as of 11:30, 17 September 2013


Full id: C752_CD4_acute_NK_chronic_CD14_Neutrophils_lymphoma



Phase1 CAGE Peaks

Hg19::chr13:42041063..42041070,+p@chr13:42041063..42041070
+
Hg19::chr4:8202186..8202194,-p@chr4:8202186..8202194
-
Hg19::chrX:1582102..1582110,+p@chrX:1582102..1582110
+
Hg19::chrX:1586094..1586111,-p@chrX:1586094..1586111
-
Hg19::chrX:1592603..1592615,-p@chrX:1592603..1592615
-
Hg19::chrX:1594302..1594330,-p@chrX:1594302..1594330
-
Hg19::chrX:1601183..1601186,-p@chrX:1601183..1601186
-
Hg19::chrX:1656050..1656053,-p6@P2RY8
Hg19::chrX:1656059..1656085,-p1@P2RY8
Hg19::chrX:1656091..1656100,-p4@P2RY8
Hg19::chrX:1780733..1780743,+p@chrX:1780733..1780743
+


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 oligopotent progenitor cell1.95e-23161
hematopoietic multipotent progenitor cell1.95e-23161
hematopoietic stem cell2.75e-22168
angioblastic mesenchymal cell2.75e-22168
hematopoietic cell6.11e-21177
nongranular leukocyte6.44e-21115
hematopoietic lineage restricted progenitor cell6.75e-20120
leukocyte3.46e-19136
classical monocyte2.30e-1842
CD14-positive, CD16-negative classical monocyte2.30e-1842
defensive cell7.81e-1648
phagocyte7.81e-1648
myeloid cell1.51e-15108
common myeloid progenitor1.51e-15108
monopoietic cell1.06e-1459
monocyte1.06e-1459
monoblast1.06e-1459
promonocyte1.06e-1459
macrophage dendritic cell progenitor3.71e-1461
myeloid leukocyte6.23e-1472
myeloid lineage restricted progenitor cell6.10e-1366
granulocyte monocyte progenitor cell1.02e-1267
lymphocyte of B lineage1.61e-1024
pro-B cell1.61e-1024
innate effector T cell9.46e-091
immature NK T cell9.46e-091
effector T cell9.46e-091
mature NK T cell9.46e-091
immature NK T cell stage IV9.46e-091
immature NK T cell stage I9.46e-091
immature NK T cell stage II9.46e-091
immature NK T cell stage III9.46e-091
antibody secreting cell1.48e-081
plasma cell1.48e-081
plasmablast1.48e-081
mesenchymal cell2.87e-08354
connective tissue cell5.09e-08361
lymphoid lineage restricted progenitor cell6.00e-0852
stuff accumulating cell6.81e-0887
lymphocyte8.91e-0853
common lymphoid progenitor8.91e-0853
nucleate cell1.88e-0755
motile cell3.84e-07386
Uber Anatomy
Ontology termp-valuen
immune system4.43e-1493
hematopoietic system3.17e-1398
blood island3.17e-1398
bone marrow5.02e-1376
bone element6.51e-1282
hemolymphoid system9.43e-12108
skeletal element1.17e-1090
skeletal system2.28e-09100
dura mater4.07e-081
future meninx4.07e-081
ectomeninx4.07e-081
future dura mater4.07e-081
connective tissue1.11e-07371
Disease
Ontology termp-valuen
bone marrow cancer1.84e-081
myeloma1.84e-081
hematologic cancer4.79e-0851
immune system cancer4.79e-0851


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)
MA0003.10.000970254
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.21986
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.729247
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.279754
MA0056.10
MA0057.10.176435
MA0058.10.265212
MA0059.10.2641
MA0060.10.38025
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.11.80505
MA0071.10.40788
MA0072.10.760818
MA0073.11.53989
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.11.34305
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.0234479
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.10.360248
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.935607
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.11.14308
MA0139.10.0922451
MA0140.11.84316
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.438224
MA0145.10.02761
MA0146.10.00165539
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.00136845
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.106997
MA0065.20.0286783
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.10.245306
MA0156.10.654264
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.761942
MA0163.10.0158063
MA0164.10.509774
MA0080.21.15057
MA0018.20.483823
MA0099.20.411824
MA0079.28.76424e-07
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
MA0442.10



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
FOXA1#316944.029607181594710.01301976979786450.0461973139199282



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.

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