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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:39, 17 September 2013


Full id: C1199_CD4_Natural_CD8_Basophils_Peripheral_mycosis_cord



Phase1 CAGE Peaks

Hg19::chr14:53619091..53619109,-p2@DDHD1
Hg19::chr1:108329128..108329139,-p@chr1:108329128..108329139
-
Hg19::chr1:25255763..25255774,-p10@RUNX3
Hg19::chr6:106546731..106546755,+p5@PRDM1
Hg19::chr6:106546786..106546802,+p6@PRDM1
Hg19::chr6:106546808..106546833,+p3@PRDM1
Hg19::chr6:106546871..106546878,+p17@PRDM1


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

GO IDGO nameFDR corrected p-value
GO:0006366transcription from RNA polymerase II promoter0.0450225075370137
GO:0050680negative regulation of epithelial cell proliferation0.0450225075370137



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
nongranular leukocyte6.00e-23115
leukocyte1.32e-21136
mature alpha-beta T cell3.40e-2118
alpha-beta T cell3.40e-2118
immature T cell3.40e-2118
mature T cell3.40e-2118
immature alpha-beta T cell3.40e-2118
T cell1.08e-2025
pro-T cell1.08e-2025
lymphoid lineage restricted progenitor cell4.31e-2052
lymphocyte1.81e-1953
common lymphoid progenitor1.81e-1953
nucleate cell2.71e-1855
hematopoietic lineage restricted progenitor cell6.09e-18120
CD8-positive, alpha-beta T cell6.22e-1411
hematopoietic cell9.87e-14177
hematopoietic stem cell2.17e-13168
angioblastic mesenchymal cell2.17e-13168
hematopoietic oligopotent progenitor cell1.52e-12161
hematopoietic multipotent progenitor cell1.52e-12161
CD4-positive, alpha-beta T cell1.81e-086
circulating cell7.92e-086
classical monocyte3.95e-0742
CD14-positive, CD16-negative classical monocyte3.95e-0742
Uber Anatomy
Ontology termp-valuen
blood5.90e-1415
haemolymphatic fluid5.90e-1415
organism substance5.90e-1415
adult organism8.64e-13114
hematopoietic system1.20e-1198
blood island1.20e-1198
hemolymphoid system1.01e-10108


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)
MA0003.11.04589
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.11.75854
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.946606
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.488614
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.340955
MA0106.11.56379
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.13.81523
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.11.59899
MA0144.10.254954
MA0145.10.276317
MA0146.10.0127148
MA0147.10.281049
MA0148.13.31745
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.21.14159
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.22.60575
MA0112.21.41281
MA0065.22.03906
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.11.40717
MA0160.10.543522
MA0161.10
MA0162.10.25944
MA0163.10.0765396
MA0164.10.678332
MA0080.20.344472
MA0018.22.64985
MA0099.21.40221
MA0079.20.07638
MA0102.21.51913
MA0258.10.687127
MA0259.10.289405
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
BATF#10538413.91874388131648.99003089381936e-050.00131242638596533
NR3C1#290848.556013332098880.0005905918520929260.00494435450426718
PAX5#507943.811180303530190.01208261681555190.0438280222839477
POU2F2#545245.203499461567160.003866714310179810.0190650446530483
TRIM28#10155410.62315716872140.0002567301005128270.00276248042112705



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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