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Coexpression cluster:C1382: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.012566646542764,0

Latest revision as of 11:43, 17 September 2013


Full id: C1382_CD14_Natural_CD8_CD4_Basophils_CD19_Neutrophils



Phase1 CAGE Peaks

Hg19::chr13:42037742..42037760,+p5@C13orf15
Hg19::chr17:39845542..39845569,-p@chr17:39845542..39845569
-
Hg19::chr18:33077635..33077682,+p@chr18:33077635..33077682
+
Hg19::chr1:198126705..198126726,-p@chr1:198126705..198126726
-
Hg19::chr2:128459741..128459755,-p@chr2:128459741..128459755
-
Hg19::chr2:128459765..128459803,-p@chr2:128459765..128459803
-


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
hematopoietic stem cell2.27e-36168
angioblastic mesenchymal cell2.27e-36168
leukocyte1.74e-35136
hematopoietic cell1.94e-35177
hematopoietic oligopotent progenitor cell9.56e-33161
hematopoietic multipotent progenitor cell9.56e-33161
nongranular leukocyte1.09e-31115
hematopoietic lineage restricted progenitor cell1.69e-31120
classical monocyte2.04e-2542
CD14-positive, CD16-negative classical monocyte2.04e-2542
defensive cell1.57e-2048
phagocyte1.57e-2048
myeloid cell7.57e-18108
common myeloid progenitor7.57e-18108
granulocyte monocyte progenitor cell1.34e-1767
myeloid leukocyte1.36e-1772
macrophage dendritic cell progenitor1.01e-1661
myeloid lineage restricted progenitor cell6.41e-1666
monopoietic cell9.55e-1659
monocyte9.55e-1659
monoblast9.55e-1659
promonocyte9.55e-1659
lymphoid lineage restricted progenitor cell2.14e-1452
lymphocyte2.63e-1453
common lymphoid progenitor2.63e-1453
nucleate cell6.74e-1455
mature alpha-beta T cell6.70e-1018
alpha-beta T cell6.70e-1018
immature T cell6.70e-1018
mature T cell6.70e-1018
immature alpha-beta T cell6.70e-1018
T cell3.31e-0825
pro-T cell3.31e-0825
native cell2.89e-07722
mesenchymal cell3.21e-07354
stuff accumulating cell5.82e-0787
B cell7.12e-0714
connective tissue cell7.29e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.26e-1898
blood island3.26e-1898
hemolymphoid system4.39e-18108
immune system4.06e-1593
bone marrow4.03e-1476
bone element4.61e-1282
skeletal element1.17e-0990
lateral plate mesoderm1.59e-08203
skeletal system5.95e-08100


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)
MA0003.10.515118
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.12.36158
MA0046.11.02569
MA0048.12.08744
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.11.35477
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.11.53717
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.11.8938
MA0147.11.57246
MA0148.10.584698
MA0149.10.612449
MA0062.21.90691
MA0035.20.621793
MA0039.20.82735
MA0138.23.01409
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.0270301
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.20.0607789
MA0102.21.58513
MA0258.10.289793
MA0259.11.6038
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
BCL3#602317.27355140186920.0004539630608098260.00422035322306546
BCLAF1#9774310.82632380506090.001772351046991060.0108890270602212
CCNT2#90544.224134384641760.007109805478875810.0296080774515854
ELF1#199753.548414965672950.003446837775721690.0175277188849254
ETS1#211346.485840614801560.001410474068463220.00916953011118769
GABPB1#255344.711789224121450.004730054311555960.0222884922507035
HEY1#2346253.366759202588090.004423827045203030.0209494909211009
HMGN3#932445.452365148900390.002729616882333770.0149875641435286
MAX#414944.301703672671410.006644923910676370.0282972154253671
PAX5#507944.446377020785220.005874733519240790.026362090487926
POLR2A#543062.147453176558070.01019570676818780.0380119736965968
POU2F2#545246.070749371828350.001815326209524520.0108941477904115
REST#597846.433352477418680.001454954223032070.00932461733549623
SIN3A#2594243.605923151210090.01273893844487140.0459406765277596
SMARCB1#6598515.21059648429782.82373084197797e-069.74901241009379e-05
TAF1#687252.785871904787740.01078636340290410.0397907882955705
TAF7#687947.622046269949280.000759279015141480.00596631864136341
TBP#690853.088975572580320.006645448275786930.0282856083659336
YY1#752854.092642291544880.001743365462849530.0107254562661724



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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