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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:34, 17 September 2013


Full id: C971_CD34_immature_Mast_CD133_CD19_Natural_Basophils



Phase1 CAGE Peaks

Hg19::chr10:12375728..12375741,-p@chr10:12375728..12375741
-
Hg19::chr12:90343644..90343653,-p@chr12:90343644..90343653
-
Hg19::chr14:89882631..89882659,+p@chr14:89882631..89882659
+
Hg19::chr1:156074228..156074251,+p@chr1:156074228..156074251
+
Hg19::chr2:232571303..232571355,+p5@PTMA
Hg19::chr2:98280747..98280764,+p2@ENST00000450072
Hg19::chr7:100027806..100027819,-p@chr7:100027806..100027819
-
Hg19::chrX:40032100..40032114,-p@chrX:40032100..40032114
-


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
leukocyte3.72e-40136
hematopoietic stem cell8.08e-33168
angioblastic mesenchymal cell8.08e-33168
hematopoietic cell4.63e-31177
hematopoietic lineage restricted progenitor cell5.32e-31120
nongranular leukocyte1.06e-29115
hematopoietic oligopotent progenitor cell9.33e-29161
hematopoietic multipotent progenitor cell9.33e-29161
lymphoid lineage restricted progenitor cell1.24e-2252
lymphocyte5.25e-2253
common lymphoid progenitor5.25e-2253
nucleate cell8.03e-2155
B cell9.79e-1514
myeloid leukocyte2.31e-1272
lymphocyte of B lineage4.37e-1124
pro-B cell4.37e-1124
classical monocyte4.48e-1142
CD14-positive, CD16-negative classical monocyte4.48e-1142
granulocyte monocyte progenitor cell1.20e-1067
mesenchymal cell1.56e-10354
intermediate monocyte2.20e-109
CD14-positive, CD16-positive monocyte2.20e-109
myeloid cell4.91e-10108
common myeloid progenitor4.91e-10108
CD4-positive, alpha-beta T cell5.25e-106
connective tissue cell6.63e-10361
motile cell2.24e-09386
T cell2.57e-0925
pro-T cell2.57e-0925
mature alpha-beta T cell4.69e-0918
alpha-beta T cell4.69e-0918
immature T cell4.69e-0918
mature T cell4.69e-0918
immature alpha-beta T cell4.69e-0918
macrophage dendritic cell progenitor5.22e-0961
defensive cell6.09e-0948
phagocyte6.09e-0948
myeloid lineage restricted progenitor cell8.04e-0966
monopoietic cell1.65e-0759
monocyte1.65e-0759
monoblast1.65e-0759
promonocyte1.65e-0759
stem cell9.91e-07441
Uber Anatomy
Ontology termp-valuen
bone marrow4.00e-1176
hematopoietic system1.55e-1098
blood island1.55e-1098
bone element1.99e-1082
connective tissue1.60e-09371
hemolymphoid system2.88e-09108
immune system5.84e-0993
skeletal element9.73e-0990
skeletal system4.71e-07100


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)
MA0003.11.66566
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.10.727045
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.11.06021
MA0061.12.19078
MA0063.10
MA0066.11.3723
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0136601
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.441522
MA0089.10
MA0090.10.391903
MA0091.11.16006
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.792149
MA0105.13.31023
MA0106.10.59853
MA0107.11.92372
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.11.60834
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.10.359385
MA0142.11.72156
MA0143.11.49284
MA0144.10.623945
MA0145.10.220937
MA0146.10.239099
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.284736
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.22.2406
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.11.64163
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.625961
MA0163.11.06699
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.916243
MA0102.21.46209
MA0258.11.7796
MA0259.11.29349
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
E2F1#186953.067118259299580.01129732364974160.0414487874887712
ESR1#2099311.53822623605790.001699321616590140.0106158302616974
FOS#235344.49897765444720.007374489916227120.0304830346062235
IRF3#3661211.74548805287240.01164488049453140.0425341752865515
NFKB1#479053.430039640121150.006880907700328230.0291405506392515
POLR2A#543082.147453176558070.002210725788971910.0127287055887555
TFAP2A#702036.194487889891860.009861483862380290.0370502738723338



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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