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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:31, 17 September 2013


Full id: C792_CD4_chronic_Whole_blood_CD19_biphenotypic_Natural



Phase1 CAGE Peaks

Hg19::chr11:118183437..118183448,-p@chr11:118183437..118183448
-
Hg19::chr11:67203465..67203500,+p@chr11:67203465..67203500
+
Hg19::chr16:68390556..68390581,+p@chr16:68390556..68390581
+
Hg19::chr6:31548335..31548356,+p@chr6:31548335..31548356
+
Hg19::chr6:31548428..31548469,+p3@AK095821
Hg19::chr6:31548438..31548449,-p@chr6:31548438..31548449
-
Hg19::chr6:31548476..31548492,-p@chr6:31548476..31548492
-
Hg19::chr6:31548554..31548577,-p@chr6:31548554..31548577
-
Hg19::chr6:31548595..31548608,-p@chr6:31548595..31548608
-
Hg19::chr6:31549373..31549385,-p@chr6:31549373..31549385
-


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
lymphoid lineage restricted progenitor cell1.49e-5552
lymphocyte2.50e-5453
common lymphoid progenitor2.50e-5453
nucleate cell5.18e-5255
mature alpha-beta T cell2.03e-3718
alpha-beta T cell2.03e-3718
immature T cell2.03e-3718
mature T cell2.03e-3718
immature alpha-beta T cell2.03e-3718
T cell6.00e-3325
pro-T cell6.00e-3325
nongranular leukocyte6.49e-26115
leukocyte8.36e-22136
hematopoietic lineage restricted progenitor cell5.12e-20120
CD8-positive, alpha-beta T cell1.05e-1911
hematopoietic stem cell3.07e-19168
angioblastic mesenchymal cell3.07e-19168
hematopoietic cell9.80e-18177
lymphocyte of B lineage1.46e-1724
pro-B cell1.46e-1724
CD4-positive, alpha-beta T cell2.21e-176
hematopoietic oligopotent progenitor cell7.85e-16161
hematopoietic multipotent progenitor cell7.85e-16161
B cell5.30e-1014
natural killer cell2.97e-093
pro-NK cell2.97e-093
naive T cell3.74e-093
single nucleate cell6.60e-093
mononuclear cell6.60e-093
regulatory T cell9.36e-072
CD4-positive, CD25-positive, alpha-beta regulatory T cell9.36e-072
naive regulatory T cell9.36e-072
Uber Anatomy
Ontology termp-valuen
blood6.38e-1815
haemolymphatic fluid6.38e-1815
organism substance6.38e-1815
hemopoietic organ2.38e-137
immune organ2.38e-137
thymus3.04e-114
hemolymphoid system gland3.04e-114
thymic region3.04e-114
pharyngeal gland3.04e-114
thymus primordium3.04e-114
pharyngeal epithelium1.62e-076


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)
MA0003.10.632731
MA0004.10.380329
MA0006.11.23783
MA0007.10.363007
MA0009.10.828613
MA0014.11.2642
MA0017.11.36636
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.697761
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.11.25863
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.802927
MA0058.10.293055
MA0059.10.79343
MA0060.10.138988
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.11.05557
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.0214747
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.55119
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.678051
MA0103.10.228129
MA0105.12.12449
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.885497
MA0113.10.532314
MA0114.10.998594
MA0115.11.06753
MA0116.11.02702
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.353333
MA0140.10.437738
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.602634
MA0146.10.243477
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.0317541
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.21.75318
MA0065.20.340764
MA0150.10.845871
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.11.12157
MA0155.11.6917
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.00711618
MA0163.10.299639
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.20.0313405
MA0102.21.36707
MA0258.11.47203
MA0259.10.191914
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
CHD2#110644.137609133646740.01136509692198320.0416623151082836
CTCFL#14069047.898589743589740.001078356575107990.00761322803675411
ETS1#211343.891504368880930.01407798708438330.0494016159231874
HDAC2#306645.36624809465050.004493045676013980.0212560788801062
MEF2A#420559.371615454822038.6760671028562e-050.00129946905514872
NFKB1#479063.29283805451630.00391275252059270.0190678904623294
PAX5#507953.334782765588910.009853624493675830.0370274057674598
RAD21#588544.142013558182530.01132276475674040.0415304568528908
SMC3#912646.017973137973140.002957963916685310.0157696168195353
THAP1#55145412.54765784114050.0001856500560886790.00224697024079795
TRIM28#1015547.436210018105010.001351406221142950.00889964779178694
USF1#739153.180749638603980.01206500641784450.0437884766914535
ZEB1#693546.755372807017540.001931556127194530.0113516285165759
ZNF143#770245.400350620891160.004390996550104770.0208100598401049
ZNF263#1012754.110920818505340.003944399225787830.0189602389074449



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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