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Coexpression cluster:C388: Difference between revisions

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

Latest revision as of 11:21, 17 September 2013


Full id: C388_CD4_CD8_cord_Peripheral_Natural_Whole_thymus



Phase1 CAGE Peaks

Hg19::chr10:102270916..102270937,-p@chr10:102270916..102270937
-
Hg19::chr10:63977682..63977689,-p@chr10:63977682..63977689
-
Hg19::chr10:63977707..63977724,-p@chr10:63977707..63977724
-
Hg19::chr10:6625733..6625740,+p2@ENST00000449648
Hg19::chr11:114189327..114189369,+p@chr11:114189327..114189369
+
Hg19::chr12:102591576..102591596,-p1@PMCH
Hg19::chr14:23006547..23006583,+p1@TRAJ7
Hg19::chr16:72033758..72033771,-p1@PKD1L3
Hg19::chr17:80851254..80851295,+p3@TBCD
Hg19::chr20:39768553..39768594,+p@chr20:39768553..39768594
+
Hg19::chr2:28203275..28203307,+p@chr2:28203275..28203307
+
Hg19::chr2:28203353..28203364,+p@chr2:28203353..28203364
+
Hg19::chr2:28837237..28837245,-p@chr2:28837237..28837245
-
Hg19::chr3:105895690..105895701,+p@chr3:105895690..105895701
+
Hg19::chr3:194209056..194209074,+p@chr3:194209056..194209074
+
Hg19::chr4:82353730..82353737,-p@chr4:82353730..82353737
-
Hg19::chr4:82353753..82353763,-p@chr4:82353753..82353763
-
Hg19::chr5:66118077..66118092,+p@chr5:66118077..66118092
+
Hg19::chr6:130455835..130455839,-p@chr6:130455835..130455839
-
Hg19::chr6:149639812..149639830,+p12@TAB2
Hg19::chr6:149639840..149639869,+p9@TAB2
Hg19::chr6:29803155..29803158,+p@chr6:29803155..29803158
+
Hg19::chr6:37249918..37249929,+p@chr6:37249918..37249929
+
Hg19::chr6:37249933..37249954,+p@chr6:37249933..37249954
+
Hg19::chrX:49122760..49122762,-p@chrX:49122760..49122762
-
Hg19::chrX:49122911..49122916,-p@chrX:49122911..49122916
-
Hg19::chrX:49122952..49122962,-p@chrX:49122952..49122962
-


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:0007218neuropeptide signaling pathway0.00508860167908128
GO:0030354melanin-concentrating hormone activity0.0103013890731043
GO:0007025beta-tubulin folding0.0103013890731043
GO:0007021tubulin folding0.0139052377329709
GO:0051087chaperone binding0.0197722629543939
GO:0007631feeding behavior0.0380792453878901



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><br><br>


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)
MA0003.11.29331e-07
MA0004.10.115462
MA0006.10.043712
MA0007.10.105458
MA0009.11.14995
MA0014.11.09125e-06
MA0017.10.0582511
MA0019.10.206961
MA0024.10.366071
MA0025.10.570597
MA0027.12.00534
MA0028.10.0494049
MA0029.11.7622
MA0030.10.372472
MA0031.10.320773
MA0038.10.176878
MA0040.11.0045
MA0041.10.125771
MA0042.10.108251
MA0043.10.453881
MA0046.10.444311
MA0048.10.0119659
MA0050.10.351951
MA0051.10.174152
MA0052.10.389861
MA0055.10.148021
MA0056.10
MA0057.10.0369704
MA0058.10.0687016
MA0059.10.240654
MA0060.10.0133608
MA0061.10.00915103
MA0063.10
MA0066.10.177154
MA0067.10.739032
MA0068.113.0876
MA0069.10.441028
MA0070.10.431528
MA0071.10.464021
MA0072.10.427724
MA0073.10.112451
MA0074.10.173668
MA0076.10.0757217
MA0077.10.421218
MA0078.10.242013
MA0081.10.240854
MA0083.10.460049
MA0084.10.916043
MA0087.11.08951
MA0088.10.0109451
MA0089.10
MA0090.10.280795
MA0091.10.373385
MA0092.10.659672
MA0093.10.171002
MA0095.10
MA0098.10
MA0100.10.546121
MA0101.10.393842
MA0103.10.648352
MA0105.10.00795696
MA0106.10.204305
MA0107.10.023874
MA0108.20.318371
MA0109.10
MA0111.10.298621
MA0113.10.2156
MA0114.10.022641
MA0115.10.668285
MA0116.10.482814
MA0117.10.486035
MA0119.10.0614144
MA0122.10.50863
MA0124.10.630319
MA0125.10.554615
MA0130.10
MA0131.10.255226
MA0132.10
MA0133.10
MA0135.10.479757
MA0136.11.62184
MA0139.10.113289
MA0140.10.459966
MA0141.10.238511
MA0142.11.45957
MA0143.10.215723
MA0144.13.38037
MA0145.10.0904308
MA0146.10.000267025
MA0147.10.108532
MA0148.10.806841
MA0149.10.145006
MA0062.20.122342
MA0035.20.150428
MA0039.20.00286767
MA0138.20.242899
MA0002.21.11033
MA0137.24.01949
MA0104.20.0630844
MA0047.20.196083
MA0112.20.0124735
MA0065.20.0952518
MA0150.10.0796342
MA0151.10
MA0152.10.915791
MA0153.10.539635
MA0154.10.0274497
MA0155.10.0703467
MA0156.11.15937
MA0157.10.275302
MA0158.10
MA0159.10.265053
MA0160.10.138224
MA0161.10
MA0162.10.00195038
MA0163.10.0543687
MA0164.10.63749
MA0080.21.50555
MA0018.20.592438
MA0099.20.91671
MA0079.21.61803e-10
MA0102.20.951693
MA0258.10.017374
MA0259.10.116092
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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