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Coexpression cluster:C542: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:25, 17 September 2013


Full id: C542_squamous_colon_pharyngeal_ductal_renal_gall_peripheral



Phase1 CAGE Peaks

Hg19::chr14:103560509..103560517,+p@chr14:103560509..103560517
+
Hg19::chr17:4699695..4699699,-p@chr17:4699695..4699699
-
Hg19::chr17:47210085..47210098,+p2@B4GALNT2
Hg19::chr17:47210125..47210136,+p1@B4GALNT2
Hg19::chr17:76533685..76533690,-p@chr17:76533685..76533690
-
Hg19::chr20:10619745..10619768,-p@chr20:10619745..10619768
-
Hg19::chr20:10619777..10619811,-p@chr20:10619777..10619811
-
Hg19::chr20:10750941..10750951,+p@chr20:10750941..10750951
+
Hg19::chr2:103353367..103353400,+p1@TMEM182
Hg19::chr2:165860476..165860511,+p@chr2:165860476..165860511
+
Hg19::chr2:188385262..188385271,+p@chr2:188385262..188385271
+
Hg19::chr3:112521361..112521367,+p1@ENST00000496067
Hg19::chr3:112521387..112521398,+p2@ENST00000519700
Hg19::chr3:112521422..112521435,+p1@ENST00000519700
Hg19::chr9:130914175..130914189,+p@chr9:130914175..130914189
+
Hg19::chr9:130915675..130915689,+p@chr9:130915675..130915689
+
Hg19::chr9:130915692..130915702,+p@chr9:130915692..130915702
+


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:0019276UDP-N-acetylgalactosamine metabolic process0.00735856827869091
GO:0006047UDP-N-acetylglucosamine metabolic process0.00735856827869091
GO:0030259lipid glycosylation0.00735856827869091
GO:0022408negative regulation of cell-cell adhesion0.0103006308464257
GO:0022407regulation of cell-cell adhesion0.0103006308464257
GO:0009225nucleotide-sugar metabolic process0.0103006308464257
GO:0007162negative regulation of cell adhesion0.0154461696665433
GO:0008376acetylgalactosaminyltransferase activity0.0154461696665433
GO:0006044N-acetylglucosamine metabolic process0.0154461696665433
GO:0006041glucosamine metabolic process0.0154461696665433
GO:0006040amino sugar metabolic process0.0164477143333733
GO:0030258lipid modification0.0191190416765635
GO:0030173integral to Golgi membrane0.0205842782151792
GO:0030155regulation of cell adhesion0.0205842782151792
GO:0031228intrinsic to Golgi membrane0.0205842782151792
GO:0008194UDP-glycosyltransferase activity0.0348461799623283
GO:0031301integral to organelle membrane0.0348461799623283
GO:0031300intrinsic to organelle membrane0.0348461799623283
GO:0005792microsome0.0348461799623283
GO:0042598vesicular fraction0.0348461799623283
GO:0006486protein amino acid glycosylation0.0348461799623283
GO:0043413biopolymer glycosylation0.0348461799623283
GO:0009101glycoprotein biosynthetic process0.0348461799623283
GO:0009100glycoprotein metabolic process0.0381502198512918
GO:0016758transferase activity, transferring hexosyl groups0.0494245767274581



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>disease_data<br>

Cell Type
Ontology termp-valuen
bladder cell4.20e-291
lower urinary tract cell4.20e-291
epithelial cell of cervix2.37e-152
Disease
Ontology termp-valuen
squamous cell carcinoma4.21e-0914
carcinoma5.42e-07106
cervical cancer6.39e-075


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)
MA0003.10.0826737
MA0004.10.221943
MA0006.10.112549
MA0007.10.208008
MA0009.10.621697
MA0014.10.0173262
MA0017.11.3589
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.664972
MA0042.10.608306
MA0043.10.621991
MA0046.10.611559
MA0048.10.345177
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.11.42965
MA0056.10
MA0057.10.164004
MA0058.10.467197
MA0059.10.465036
MA0060.10.0509127
MA0061.10.640118
MA0063.10
MA0066.11.48446
MA0067.10.924196
MA0068.10.803993
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.10.205609
MA0074.10.298586
MA0076.10.493997
MA0077.10.586275
MA0078.10.382364
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.755104
MA0089.10
MA0090.10.518617
MA0091.10.223914
MA0092.10.570207
MA0093.10.366841
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.372085
MA0103.10.34743
MA0105.10.7537
MA0106.10.33677
MA0107.10.551112
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.11.90309
MA0115.10.850405
MA0116.10.0765991
MA0117.10.656858
MA0119.10.142224
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.830767
MA0139.10.0351037
MA0140.10.269307
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.10.0651126
MA0145.10.577453
MA0146.10.201639
MA0147.10.269778
MA0148.10.240905
MA0149.10.261654
MA0062.20.148712
MA0035.20.268747
MA0039.20.339706
MA0138.21.7676
MA0002.22.02975
MA0137.22.53112
MA0104.20.188874
MA0047.20.87164
MA0112.20.790396
MA0065.20.593175
MA0150.10.170499
MA0151.10
MA0152.10.753898
MA0153.10.714423
MA0154.10.137179
MA0155.11.35621
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.270712
MA0160.10.252705
MA0161.10
MA0162.10.155087
MA0163.10.55621
MA0164.10.361105
MA0080.20.11444
MA0018.20.337929
MA0099.20.27482
MA0079.20.148384
MA0102.21.14323
MA0258.10.476351
MA0259.10.0828875
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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