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

Latest revision as of 11:37, 17 September 2013


Full id: C1103_CD19_CD4_CD8_Whole_blood_Burkitt_thymus



Phase1 CAGE Peaks

Hg19::chr10:1089744..1089786,-p@chr10:1089744..1089786
-
Hg19::chr14:50443908..50443920,+p@chr14:50443908..50443920
+
Hg19::chr1:101491406..101491471,+p1@ENST00000421013
p1@ENST00000453011
p1@uc001dua.2
p1@uc001dub.2
Hg19::chr6:31548841..31548854,-p@chr6:31548841..31548854
-
Hg19::chr6:31550094..31550103,-p3@LTB
Hg19::chr6:31550108..31550121,-p2@LTB
Hg19::chr6:31550192..31550207,-p1@LTB


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:0005164tumor necrosis factor receptor binding0.0102584481337572
GO:0032813tumor necrosis factor receptor superfamily binding0.0102584481337572



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
leukocyte1.00e-61136
nongranular leukocyte2.10e-57115
hematopoietic stem cell4.34e-55168
angioblastic mesenchymal cell4.34e-55168
hematopoietic lineage restricted progenitor cell2.59e-51120
hematopoietic cell1.85e-50177
hematopoietic oligopotent progenitor cell6.95e-49161
hematopoietic multipotent progenitor cell6.95e-49161
lymphocyte1.17e-4153
common lymphoid progenitor1.17e-4153
lymphoid lineage restricted progenitor cell9.19e-4152
nucleate cell1.78e-3955
mature alpha-beta T cell4.28e-2018
alpha-beta T cell4.28e-2018
immature T cell4.28e-2018
mature T cell4.28e-2018
immature alpha-beta T cell4.28e-2018
lymphocyte of B lineage4.66e-2024
pro-B cell4.66e-2024
T cell6.63e-1925
pro-T cell6.63e-1925
myeloid leukocyte8.47e-1772
granulocyte monocyte progenitor cell5.67e-1667
monopoietic cell2.07e-1559
monocyte2.07e-1559
monoblast2.07e-1559
promonocyte2.07e-1559
myeloid lineage restricted progenitor cell2.90e-1566
B cell8.37e-1514
defensive cell9.89e-1548
phagocyte9.89e-1548
classical monocyte1.30e-1442
CD14-positive, CD16-negative classical monocyte1.30e-1442
macrophage dendritic cell progenitor1.54e-1461
myeloid cell2.84e-14108
common myeloid progenitor2.84e-14108
CD8-positive, alpha-beta T cell6.11e-1311
mesenchymal cell4.30e-10354
intermediate monocyte1.71e-099
CD14-positive, CD16-positive monocyte1.71e-099
connective tissue cell2.25e-09361
CD4-positive, alpha-beta T cell6.58e-086
motile cell2.98e-07386
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.99e-26108
hematopoietic system2.87e-2598
blood island2.87e-2598
immune system2.56e-1893
bone marrow1.50e-1376
bone element1.11e-1182
blood1.80e-1015
haemolymphatic fluid1.80e-1015
organism substance1.80e-1015
skeletal element1.25e-0990
connective tissue2.04e-08371
skeletal system1.35e-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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.610358
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.12.03099
MA0031.11.8966
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
MA0055.10.158296
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.11.09187
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.12.38293
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.12.48383
MA0103.10.88373
MA0105.10.340955
MA0106.10.648997
MA0107.11.3795
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.269076
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
MA0141.11.83545
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.581146
MA0146.10.162729
MA0147.10.281049
MA0148.12.2535
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.854285
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.22.60575
MA0112.20.0758925
MA0065.22.65697
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.12.27082
MA0155.10.250175
MA0156.10.36627
MA0157.11.77267
MA0158.10
MA0159.10.281681
MA0160.12.30417
MA0161.10
MA0162.10.0249953
MA0163.11.30651
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.21.82808
MA0102.21.51913
MA0258.10.245543
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
ELF1#199753.041498542005380.009719562269370750.0365552005420005
NFKB1#479053.92004530299560.003036581424484610.0161147117577108
POLR2A#543072.147453176558070.004747636447610280.0223199821270299
ZEB1#693549.650532581453630.0003718916645689250.00369799043662896



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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