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Coexpression cluster:C965: Difference between revisions

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{{Coexpression_clusters
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|full_id=C965_smooth_Osteoblast_Adipocyte_aorta_penis_Preadipocyte_normal
|id=C965
}}

Latest revision as of 11:34, 17 September 2013


Full id: C965_smooth_Osteoblast_Adipocyte_aorta_penis_Preadipocyte_normal



Phase1 CAGE Peaks

Hg19::chrX:153593573..153593599,-p6@FLNA
Hg19::chrX:153594489..153594515,-p@chrX:153594489..153594515
-
Hg19::chrX:153594978..153595014,-p@chrX:153594978..153595014
-
Hg19::chrX:153595130..153595149,-p@chrX:153595130..153595149
-
Hg19::chrX:153595810..153595838,-p@chrX:153595810..153595838
-
Hg19::chrX:153595864..153595919,-p@chrX:153595864..153595919
-
Hg19::chrX:153596060..153596111,-p@chrX:153596060..153596111
-
Hg19::chrX:153596325..153596358,-p@chrX:153596325..153596358
-
Hg19::chrX:153599349..153599396,-p5@FLNA


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
somatic cell3.63e-20588
animal cell3.69e-18679
eukaryotic cell3.69e-18679
native cell5.37e-13722
multi fate stem cell5.15e-12427
somatic stem cell8.04e-12433
defensive cell3.20e-1148
phagocyte3.20e-1148
classical monocyte4.53e-1142
CD14-positive, CD16-negative classical monocyte4.53e-1142
stem cell6.03e-11441
fibroblast9.73e-1176
mesodermal cell7.08e-09121
stuff accumulating cell1.03e-0887
embryonic cell2.82e-07250
connective tissue cell3.23e-07361
monopoietic cell3.56e-0759
monocyte3.56e-0759
monoblast3.56e-0759
promonocyte3.56e-0759
mesenchymal cell4.69e-07354
smooth muscle cell7.06e-0743
smooth muscle myoblast7.06e-0743
Uber Anatomy
Ontology termp-valuen
mesoderm4.39e-18315
mesoderm-derived structure4.39e-18315
presumptive mesoderm4.39e-18315
lateral plate mesoderm1.12e-11203
musculoskeletal system1.42e-08167
artery9.60e-0842
arterial blood vessel9.60e-0842
arterial system9.60e-0842
vasculature1.79e-0778
vascular system1.79e-0778
epithelial vesicle1.89e-0778
connective tissue5.35e-07371
cardiovascular system7.10e-07109
epithelial tube open at both ends9.63e-0759
blood vessel9.63e-0759
blood vasculature9.63e-0759
vascular cord9.63e-0759
vessel9.64e-0768


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)
MA0003.11.64541
MA0004.10.415381
MA0006.10.733408
MA0007.11.02827
MA0009.10.870971
MA0014.10.367355
MA0017.11.47956
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.767002
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.11.95759
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.851955
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.11.88564
MA0092.10.993944
MA0093.10.73976
MA0095.10
MA0098.10
MA0100.11.30927
MA0101.10.271368
MA0103.10.714036
MA0105.12.36395
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.11.10197
MA0115.11.11137
MA0116.13.30706
MA0117.10.908433
MA0119.11.50574
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.12.56675
MA0140.10.474342
MA0141.10.861836
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.706237
MA0146.14.07186
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.00489248
MA0138.20.608783
MA0002.20.905786
MA0137.20.28622
MA0104.20.486672
MA0047.20.542971
MA0112.20.674448
MA0065.20.408099
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.11.27456
MA0155.11.43005
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.11.15068
MA0161.10
MA0162.10.0107891
MA0163.11.18882
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.000337902
MA0102.21.41188
MA0258.10.180288
MA0259.10.624802
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
POLR2A#543092.147453176558070.001029412892608020.00729084857528072



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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