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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.00853123773455933,0.

Latest revision as of 11:24, 17 September 2013


Full id: C500_Neutrophils_Monocytederived_blood_CD14_Eosinophils_lung_mixed



Phase1 CAGE Peaks

Hg19::chr12:65090856..65090873,+p@chr12:65090856..65090873
+
Hg19::chr15:45007619..45007649,+p6@B2M
Hg19::chr15:45007659..45007713,+p3@B2M
Hg19::chr15:45007740..45007774,+p5@B2M
Hg19::chr15:45007776..45007836,+p2@B2M
Hg19::chr15:45009798..45009900,+p@chr15:45009798..45009900
+
Hg19::chr15:45009902..45010022,+p@chr15:45009902..45010022
+
Hg19::chr1:203276836..203276855,+p@chr1:203276836..203276855
+
Hg19::chr6:29691484..29691495,+p3@HLA-F
Hg19::chr6:30458007..30458044,+p@chr6:30458007..30458044
+
Hg19::chr6:30458081..30458117,+p@chr6:30458081..30458117
+
Hg19::chr6:30458196..30458253,+p@chr6:30458196..30458253
+
Hg19::chr6:30460680..30460737,+p@chr6:30460680..30460737
+
Hg19::chr6:31239406..31239455,+p@chr6:31239406..31239455
+
Hg19::chr6:31321862..31321941,-p1@X07061
p1@X07062
Hg19::chr6:31322867..31322902,+p@chr6:31322867..31322902
+
Hg19::chr6:31322916..31322974,-p4@HLA-B
Hg19::chr6:31323216..31323285,-p3@HLA-C
p5@HLA-B
Hg19::chr6:31324641..31324664,-p10@HLA-B


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

p.valueFDRnGenesnPathwayName
0.0001517463875231860.008004621941848052204Endocytosis (KEGG):04144
8.87028067484744e-050.005104443333798572156Phagosome (KEGG):04145
6.73840783266509e-050.0042654121580772136Cell adhesion molecules (CAMs) (KEGG):04514
1.96249599285332e-086.21129981738076e-06378Antigen processing and presentation (KEGG):04612
7.28240379719336e-060.000768293600603899245Type I diabetes mellitus (KEGG):04940
1.05241687813521e-050.000951685548370838254Autoimmune thyroid disease (KEGG):05320
5.45153351157612e-060.000768293600603899239Allograft rejection (KEGG):05330
6.64274556874299e-060.000768293600603899243Graft-versus-host disease (KEGG):05332
1.87899740683929e-050.00132156150947697272Viral myocarditis (KEGG):05416
1.48230348787841e-050.00117287263478379264Proteasome Degradation (Wikipathways):WP183
5.70320151504265e-060.0007682936006038993511Signaling in Immune system (Reactome):REACT_6900
5.37212511845661e-093.40055519998304e-06351{HLA-A,53} (Static Module):NA



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:0002474antigen processing and presentation of peptide antigen via MHC class I3.44283425591547e-07
GO:0048002antigen processing and presentation of peptide antigen3.44283425591547e-07
GO:0042612MHC class I protein complex2.48279173867282e-06
GO:0042611MHC protein complex7.44220434057843e-06
GO:0019882antigen processing and presentation8.68789839607204e-06
GO:0032393MHC class I receptor activity1.03087902489797e-05
GO:0006955immune response0.000146634857782203
GO:0002376immune system process0.000203303733848579
GO:0044459plasma membrane part0.000810460688395914
GO:0043234protein complex0.00146544028199587
GO:0005886plasma membrane0.0029844998842909
GO:0032991macromolecular complex0.0029844998842909
GO:0004888transmembrane receptor activity0.0188521394295296
GO:0044425membrane part0.0201582891042318
GO:0004872receptor activity0.0354197492238477
GO:0016020membrane0.0354197492238477
GO:0004871signal transducer activity0.0442459626345693
GO:0060089molecular transducer activity0.0442459626345693



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
leukocyte2.94e-45136
nongranular leukocyte2.60e-40115
hematopoietic lineage restricted progenitor cell9.46e-36120
hematopoietic stem cell3.14e-31168
angioblastic mesenchymal cell3.14e-31168
hematopoietic cell4.59e-30177
hematopoietic oligopotent progenitor cell6.78e-30161
hematopoietic multipotent progenitor cell6.78e-30161
defensive cell1.44e-2848
phagocyte1.44e-2848
myeloid leukocyte1.98e-2872
macrophage dendritic cell progenitor5.28e-2761
monopoietic cell2.27e-2659
monocyte2.27e-2659
monoblast2.27e-2659
promonocyte2.27e-2659
classical monocyte2.94e-2542
CD14-positive, CD16-negative classical monocyte2.94e-2542
granulocyte monocyte progenitor cell1.35e-2367
myeloid lineage restricted progenitor cell7.00e-2266
myeloid cell1.81e-16108
common myeloid progenitor1.81e-16108
mesenchymal cell1.04e-15354
connective tissue cell5.69e-15361
multi fate stem cell3.68e-13427
lymphocyte5.11e-1353
common lymphoid progenitor5.11e-1353
lymphoid lineage restricted progenitor cell6.15e-1352
somatic stem cell1.29e-11433
nucleate cell2.36e-1155
stem cell5.67e-11441
stuff accumulating cell2.04e-0987
motile cell3.34e-09386
mature alpha-beta T cell3.46e-0918
alpha-beta T cell3.46e-0918
immature T cell3.46e-0918
mature T cell3.46e-0918
immature alpha-beta T cell3.46e-0918
T cell5.78e-0825
pro-T cell5.78e-0825
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.78e-29108
hematopoietic system6.19e-2998
blood island6.19e-2998
immune system2.32e-2293
bone marrow3.36e-2176
bone element1.21e-1782
connective tissue8.02e-15371
skeletal element1.36e-1490
lateral plate mesoderm1.31e-13203
skeletal system1.06e-12100
mesoderm6.15e-09315
mesoderm-derived structure6.15e-09315
presumptive mesoderm6.15e-09315
musculoskeletal system1.45e-08167
blood4.97e-0815
haemolymphatic fluid4.97e-0815
organism substance4.97e-0815


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)
MA0003.10.0417237
MA0004.10.193314
MA0006.10.308609
MA0007.10.532323
MA0009.11.41914
MA0014.10.0512398
MA0017.10.114723
MA0019.10.824541
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.11.23309
MA0031.11.11067
MA0038.10.269828
MA0040.10.507819
MA0041.10.595574
MA0042.10.183918
MA0043.10.580321
MA0046.10.570066
MA0048.10.0472517
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.106762
MA0056.10
MA0057.10.254333
MA0058.10.12994
MA0059.10.129144
MA0060.10.0387582
MA0061.10.290613
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.12.27454
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.10.552241
MA0073.11.63857
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.915792
MA0081.10.129245
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.398465
MA0089.10
MA0090.10.149167
MA0091.10.195166
MA0092.10.168981
MA0093.10.313082
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.0959778
MA0103.10.295078
MA0105.10.220534
MA0106.10.302526
MA0107.10.0591705
MA0108.20.432749
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.10.0569149
MA0115.10.805883
MA0116.11.74683
MA0117.10.614633
MA0119.10.119385
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.10.494048
MA0140.10.238066
MA0141.10.128074
MA0142.11.05085
MA0143.10.315941
MA0144.10.0508083
MA0145.10.00353814
MA0146.10.00163852
MA0147.10.0623218
MA0148.11.14208
MA0149.10.230803
MA0062.20.116085
MA0035.20.237534
MA0039.20.653922
MA0138.20.347473
MA0002.20.324376
MA0137.20.105044
MA0104.20.0384802
MA0047.22.21363
MA0112.20.421916
MA0065.20.468021
MA0150.10.145358
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.10.0342743
MA0155.10.124291
MA0156.10.703429
MA0157.11.77115
MA0158.10
MA0159.10.487475
MA0160.10.632864
MA0161.10
MA0162.10.177141
MA0163.10.551009
MA0164.10.32594
MA0080.20.0942207
MA0018.20.819991
MA0099.20.243305
MA0079.20.207401
MA0102.21.09681
MA0258.11.08978
MA0259.10.0662172
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
CTCF#10664102.821187564776330.000897037362883790.00667562242712128
POLR2A#5430182.034429325160281.12471092130166e-050.000287760127167623
RFX5#599363.804603419114240.003431185083611320.0174608750644293
WRNIP1#56897211.55999624730270.01278646128291030.0460103786495957



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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