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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:26, 17 September 2013


Full id: C575_embryonic_CD14_CD34_immature_chorionic_Mast_testis



Phase1 CAGE Peaks

Hg19::chr10:106008834..106008840,+p@chr10:106008834..106008840
+
Hg19::chr10:132517789..132517796,+p@chr10:132517789..132517796
+
Hg19::chr10:81088710..81088726,+p@chr10:81088710..81088726
+
Hg19::chr12:111842525..111842550,+p@chr12:111842525..111842550
+
Hg19::chr12:90354099..90354111,-p@chr12:90354099..90354111
-
Hg19::chr17:76858299..76858316,+p@chr17:76858299..76858316
+
Hg19::chr19:55919546..55919557,-p5@UBE2S
Hg19::chr22:30602042..30602074,+p@chr22:30602042..30602074
+
Hg19::chr5:1082038..1082051,-p4@SLC12A7
Hg19::chr5:1138370..1138374,-p@chr5:1138370..1138374
-
Hg19::chr6:126240167..126240193,-p@chr6:126240167..126240193
-
Hg19::chr6:160137409..160137424,+p@chr6:160137409..160137424
+
Hg19::chr6:30685210..30685218,+p@chr6:30685210..30685218
+
Hg19::chr8:125283938..125283961,+p2@ENST00000517482
Hg19::chr9:38170884..38170888,-p@chr9:38170884..38170888
-


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:0015379potassium:chloride symporter activity0.0141286590560376
GO:0015377cation:chloride symporter activity0.0211904930526434
GO:0015296anion:cation symporter activity0.0458944863739359



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
classical monocyte1.66e-10642
CD14-positive, CD16-negative classical monocyte1.66e-10642
defensive cell1.99e-9248
phagocyte1.99e-9248
monopoietic cell1.04e-7259
monocyte1.04e-7259
monoblast1.04e-7259
promonocyte1.04e-7259
macrophage dendritic cell progenitor3.66e-7061
myeloid leukocyte4.05e-6772
myeloid lineage restricted progenitor cell1.83e-6466
granulocyte monocyte progenitor cell2.00e-6367
stuff accumulating cell3.27e-4887
myeloid cell8.02e-43108
common myeloid progenitor8.02e-43108
nongranular leukocyte8.52e-40115
leukocyte1.88e-37136
hematopoietic lineage restricted progenitor cell2.42e-35120
hematopoietic stem cell4.33e-29168
angioblastic mesenchymal cell4.33e-29168
hematopoietic oligopotent progenitor cell1.28e-28161
hematopoietic multipotent progenitor cell1.28e-28161
hematopoietic cell2.81e-27177
mesenchymal cell3.67e-11354
connective tissue cell8.26e-11361
motile cell1.44e-09386
multi fate stem cell4.76e-08427
somatic stem cell7.71e-08433
basophil1.41e-073
stem cell1.44e-07441
Uber Anatomy
Ontology termp-valuen
bone marrow2.77e-5576
bone element7.75e-5182
hematopoietic system1.01e-4798
blood island1.01e-4798
immune system2.63e-4793
skeletal element8.10e-4690
hemolymphoid system9.50e-43108
skeletal system1.16e-40100
musculoskeletal system6.35e-22167
lateral plate mesoderm8.67e-20203
mesoderm2.32e-11315
mesoderm-derived structure2.32e-11315
presumptive mesoderm2.32e-11315
connective tissue2.50e-10371


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)
MA0003.10.00512623
MA0004.10.256222
MA0006.10.842675
MA0007.10.67744
MA0009.10.669377
MA0014.10.0332175
MA0017.10.494446
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.11.2891
MA0038.10.904297
MA0040.10.594421
MA0041.10.746198
MA0042.10.687159
MA0043.10.669676
MA0046.10.659066
MA0048.10.0212749
MA0050.10.688784
MA0051.11.60805
MA0052.10.598036
MA0055.10.0510304
MA0056.10
MA0057.10.688135
MA0058.10.182945
MA0059.10.536577
MA0060.15.99394
MA0061.13.39881
MA0063.10
MA0066.11.62204
MA0067.10.975379
MA0068.10.964815
MA0069.11.57719
MA0070.10.644843
MA0071.11.50438
MA0072.10.640598
MA0073.18.00756e-06
MA0074.10.337035
MA0076.10.567195
MA0077.10.633326
MA0078.10.424186
MA0081.10.536866
MA0083.11.62113
MA0084.11.15904
MA0087.10.63829
MA0088.10.244241
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.228476
MA0093.10.431889
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.13.43892
MA0103.10.411001
MA0105.11.70112
MA0106.10.37688
MA0107.16.79331
MA0108.20.515791
MA0109.10
MA0111.10.617603
MA0113.10.39123
MA0114.10.30732
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.71772
MA0140.10.30631
MA0141.10.533493
MA0142.10.489543
MA0143.10.391385
MA0144.10.596391
MA0145.10.478485
MA0146.10.0247789
MA0147.10.0991954
MA0148.10.758022
MA0149.10.298252
MA0062.20.425026
MA0035.20.305721
MA0039.20.072333
MA0138.20.425279
MA0002.20.220677
MA0137.20.465392
MA0104.20.236755
MA0047.20.366327
MA0112.20.124752
MA0065.20.0514203
MA0150.10.582537
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.367546
MA0155.10.240806
MA0156.10.91467
MA0157.11.17385
MA0158.10
MA0159.10.0995776
MA0160.11.43316
MA0161.10
MA0162.10.0065085
MA0163.10.0128736
MA0164.11.03839
MA0080.20.851709
MA0018.20.378086
MA0099.22.30989
MA0079.20.00235582
MA0102.21.1957
MA0258.10.569952
MA0259.10.104286
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
FOS#235363.599182123557760.003862286837325890.0190495100355834
FOSL1#806137.94271594327460.005785445903376980.0260139572352344
FOSL2#235544.514720161216450.009808741154451470.0368680312902094
JUN#372554.170943064112110.004945731421922860.0231087707576146
JUNB#372648.16283537595230.001162842816154370.00794960665551785
NFYA#480044.913488186621470.007300144479678050.0301960390238463
SIRT6#51548330.7276807980050.0001180432296896320.00160357919687246
STAT3#677474.909083665338650.0002260185316605590.00249473149736812
TRIM28#1015556.196841681754170.0008567651390713570.00644898698086295



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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