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Coexpression cluster:C862: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.187245577268637,

Latest revision as of 11:32, 17 September 2013


Full id: C862_renal_Urothelial_Small_Esophageal_colon_Prostate_amniotic



Phase1 CAGE Peaks

Hg19::chr8:134250642..134250649,-p@chr8:134250642..134250649
-
Hg19::chr8:134250840..134250883,-p@chr8:134250840..134250883
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Hg19::chr8:134251023..134251151,-p@chr8:134251023..134251151
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Hg19::chr8:134260979..134261020,-p6@NDRG1
Hg19::chr8:134262711..134262736,-p8@NDRG1
Hg19::chr8:134262744..134262771,-p3@NDRG1
Hg19::chr8:134269060..134269089,-p@chr8:134269060..134269089
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Hg19::chr8:134270630..134270670,-p@chr8:134270630..134270670
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Hg19::chr8:134276816..134276849,-p2@NDRG1
Hg19::chr8:134309488..134309503,-p1@NDRG1


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
classical monocyte4.25e-1142
CD14-positive, CD16-negative classical monocyte4.25e-1142
defensive cell1.52e-0948
phagocyte1.52e-0948
monopoietic cell6.23e-0759
monocyte6.23e-0759
monoblast6.23e-0759
promonocyte6.23e-0759
macrophage dendritic cell progenitor8.63e-0761
Uber Anatomy
Ontology termp-valuen
adult organism8.12e-14114
organ9.43e-12503
anatomical system1.39e-09624
anatomical group2.59e-09625
embryonic structure7.19e-09564
germ layer1.53e-08560
germ layer / neural crest1.53e-08560
embryonic tissue1.53e-08560
presumptive structure1.53e-08560
germ layer / neural crest derived structure1.53e-08560
epiblast (generic)1.53e-08560
multi-cellular organism1.88e-08656
developing anatomical structure6.54e-08581
embryo4.33e-07592
neural tube8.33e-0756
neural rod8.33e-0756
future spinal cord8.33e-0756
neural keel8.33e-0756


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)
MA0003.10.312279
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.11.93562
MA0014.10.0216849
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
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
MA0050.10.965046
MA0051.11.19169
MA0052.10.753928
MA0055.10.867653
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.000749839
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
MA0103.10.646502
MA0105.10.422512
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.998594
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.12.13645
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
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.11.35344
MA0146.10.243477
MA0147.10.184931
MA0148.10.403564
MA0149.11.09589
MA0062.20.366815
MA0035.20.437071
MA0039.20.936681
MA0138.20.569505
MA0002.20.407187
MA0137.20.710884
MA0104.20.428616
MA0047.20.504873
MA0112.20.904106
MA0065.20.147044
MA0150.10.845871
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.545933
MA0156.10.715501
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.11.07255
MA0161.10
MA0162.10.229496
MA0163.10.299639
MA0164.11.34364
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.20.300798
MA0102.21.36707
MA0258.10.919347
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

No analysis results for this cluster

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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