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Coexpression cluster:C1822: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1822_CD14_CD8_Neutrophils_Natural_Renal_Endothelial_acute
|id=C1822
|ontology_enrichment_celltype=CL:0002371!2.65e-35!591;CL:0000048!4.77e-33!430;CL:0000723!2.80e-32!436;CL:0000034!5.05e-30!444;CL:0000144!9.76e-30!625;CL:0000134!7.81e-28!358;CL:0002320!9.32e-28!365;CL:0000003!2.90e-24!722;CL:0002057!2.66e-22!42;CL:0000766!3.07e-22!76;CL:0000763!3.01e-21!112;CL:0000049!3.01e-21!112;CL:0000988!3.50e-21!182;CL:0000037!6.02e-21!172;CL:0000566!6.02e-21!172;CL:0002032!1.61e-20!165;CL:0000837!1.61e-20!165;CL:0000219!3.38e-20!390;CL:0000738!1.28e-18!140;CL:0000557!1.67e-18!71;CL:0000860!2.65e-18!45;CL:0002009!3.98e-18!65;CL:0002194!5.54e-18!63;CL:0000576!5.54e-18!63;CL:0000040!5.54e-18!63;CL:0000559!5.54e-18!63;CL:0000839!2.93e-17!70;CL:0000548!3.36e-17!679;CL:0000004!3.36e-17!679;CL:0000255!3.36e-17!679;CL:0000012!5.78e-17!682;CL:0002087!7.78e-17!119;CL:0002031!7.06e-16!124;CL:0000063!1.17e-14!578;CL:0000222!7.63e-09!119;CL:0000115!2.03e-07!35;CL:0000359!7.53e-07!32
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!1.41e-33!216;UBERON:0002384!1.28e-25!375;UBERON:0002390!1.40e-19!102;UBERON:0003061!1.40e-19!102;UBERON:0002193!9.11e-19!112;UBERON:0002371!6.02e-17!80;UBERON:0001474!3.04e-16!86;UBERON:0002204!1.58e-15!167;UBERON:0004535!4.08e-15!110;UBERON:0001009!4.14e-14!113;UBERON:0001981!6.61e-13!60;UBERON:0007500!6.61e-13!60;UBERON:0004537!6.61e-13!60;UBERON:0006965!6.61e-13!60;UBERON:0002405!1.12e-12!115;UBERON:0004872!1.44e-12!84;UBERON:0001637!1.52e-12!42;UBERON:0003509!1.52e-12!42;UBERON:0004572!1.52e-12!42;UBERON:0004765!1.98e-12!101;UBERON:0001434!1.98e-12!101;UBERON:0000055!1.04e-11!69;UBERON:0002049!1.26e-11!79;UBERON:0007798!1.26e-11!79;UBERON:0004573!1.17e-09!33;UBERON:0004571!1.17e-09!33;UBERON:0003914!9.27e-08!118
}}

Latest revision as of 11:52, 17 September 2013


Full id: C1822_CD14_CD8_Neutrophils_Natural_Renal_Endothelial_acute



Phase1 CAGE Peaks

Hg19::chr19:41858620..41858632,-p13@TGFB1
Hg19::chr19:41858640..41858665,-p6@TGFB1
Hg19::chr19:41859298..41859309,-p4@TGFB1
Hg19::chr19:41859532..41859555,+p@chr19:41859532..41859555
+
Hg19::chr19:41859814..41859837,-p1@TGFB1


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
somatic cell1.39e-34588
multi fate stem cell7.63e-33427
somatic stem cell3.49e-32433
stem cell1.57e-30441
mesenchymal cell2.49e-27354
connective tissue cell6.62e-27361
myeloid leukocyte1.70e-2472
native cell4.75e-24722
defensive cell6.32e-2448
phagocyte6.32e-2448
myeloid cell4.51e-23108
common myeloid progenitor4.51e-23108
hematopoietic stem cell2.74e-22168
angioblastic mesenchymal cell2.74e-22168
classical monocyte4.46e-2242
CD14-positive, CD16-negative classical monocyte4.46e-2242
hematopoietic cell5.37e-22177
macrophage dendritic cell progenitor8.68e-2261
hematopoietic oligopotent progenitor cell1.19e-21161
hematopoietic multipotent progenitor cell1.19e-21161
monopoietic cell1.38e-2159
monocyte1.38e-2159
monoblast1.38e-2159
promonocyte1.38e-2159
granulocyte monocyte progenitor cell3.43e-2167
leukocyte3.50e-20136
motile cell5.53e-20386
myeloid lineage restricted progenitor cell1.07e-1966
nongranular leukocyte7.78e-19115
animal cell2.64e-17679
eukaryotic cell2.64e-17679
hematopoietic lineage restricted progenitor cell3.24e-17120
stuff accumulating cell2.15e-0987
mesodermal cell2.41e-08121
endothelial cell3.27e-0736
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm3.32e-34203
connective tissue4.59e-25371
hematopoietic system4.35e-2198
blood island4.35e-2198
hemolymphoid system1.51e-20108
mesoderm7.43e-20315
mesoderm-derived structure7.43e-20315
presumptive mesoderm7.43e-20315
bone marrow6.58e-1976
bone element2.54e-1882
immune system1.78e-1793
skeletal element1.12e-1590
musculoskeletal system1.45e-15167
cardiovascular system4.07e-14109
skeletal system1.85e-13100
circulatory system2.23e-13112
epithelial tube open at both ends1.30e-1159
blood vessel1.30e-1159
blood vasculature1.30e-1159
vascular cord1.30e-1159
splanchnic layer of lateral plate mesoderm2.37e-1183
artery3.76e-1142
arterial blood vessel3.76e-1142
arterial system3.76e-1142
vasculature6.55e-1178
vascular system6.55e-1178
vessel1.29e-1068
systemic artery1.74e-0833
systemic arterial system1.74e-0833


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)
MA0003.15.59986
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.11.9468
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.5062
MA0056.10
MA0057.11.66737
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.11.44118
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.11.65981
MA0072.11.0812
MA0073.10.0469445
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.11.52322
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.15.61073
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.13.62647
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.12.13391
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.868598
MA0146.12.33916
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.21.41923
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.21.50443
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.13.79383
MA0155.13.30401
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.19.23128
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.27.22083
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
CTCFL#140690311.84788461538460.001201770348538230.00815169795615926
EBF1#187947.12517347725520.0007230531046774210.00577110761936608
GTF2B#2959212.77753197372970.00919936089559720.0347891535132446
NFKB1#479055.488063424193840.0002008162847462320.00239118138896496
RAD21#588536.21302033727380.007751055068811640.0318956832281962
SIN3A#2594244.327107781452110.004977052855762880.0232447197568652
SMC3#912639.02695970695970.002650964449467550.0146395979345358
ZNF143#770238.100525931336740.003624870512090980.018333067865001



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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