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Coexpression cluster:C601: Difference between revisions

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

Latest revision as of 11:26, 17 September 2013


Full id: C601_endometrial_clear_thyroid_kidney_Renal_serous_endometrioid



Phase1 CAGE Peaks

Hg19::chr18:43233616..43233624,+p@chr18:43233616..43233624
+
Hg19::chr18:43233914..43233930,+p@chr18:43233914..43233930
+
Hg19::chr19:12758382..12758427,-p3@MAN2B1
Hg19::chr1:197927638..197927639,-p@chr1:197927638..197927639
-
Hg19::chr1:81428697..81428704,-p@chr1:81428697..81428704
-
Hg19::chr21:30550414..30550419,+p@chr21:30550414..30550419
+
Hg19::chr2:191709136..191709144,-p@chr2:191709136..191709144
-
Hg19::chr3:190105820..190105829,+p3@CLDN16
Hg19::chr3:190105935..190105966,+p1@CLDN16
Hg19::chr3:190106002..190106011,+p4@CLDN16
Hg19::chr3:190106022..190106042,+p2@CLDN16
Hg19::chr3:190109013..190109017,+p@chr3:190109013..190109017
+
Hg19::chr4:56458309..56458322,-p3@PDCL2
Hg19::chr5:13407920..13407929,-p@chr5:13407920..13407929
-
Hg19::chr6:122974486..122974510,+p@chr6:122974486..122974510
+


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:0015095magnesium ion transmembrane transporter activity0.00553388769969308
GO:0006517protein deglycosylation0.00553388769969308
GO:0004559alpha-mannosidase activity0.01844412029571
GO:0006013mannose metabolic process0.0199173041198385
GO:0006516glycoprotein catabolic process0.0199173041198385
GO:0016338calcium-independent cell-cell adhesion0.0202849484648906
GO:0015923mannosidase activity0.0270378374055664
GO:0007588excretion0.0270378374055664
GO:0007611learning and/or memory0.0270378374055664
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.0298601220329419
GO:0005923tight junction0.0428867924004245
GO:0043296apical junction complex0.0428867924004245
GO:0016327apicolateral plasma membrane0.0428867924004245
GO:0006875cellular metal ion homeostasis0.0428867924004245
GO:0055065metal ion homeostasis0.0428867924004245
GO:0050954sensory perception of mechanical stimulus0.0428867924004245
GO:0007605sensory perception of sound0.0428867924004245
GO:0005911intercellular junction0.0466783910941187
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0466783910941187
GO:0030003cellular cation homeostasis0.0466783910941187
GO:0005764lysosome0.0466783910941187
GO:0000323lytic vacuole0.0466783910941187
GO:0055080cation homeostasis0.0466783910941187
GO:0009100glycoprotein metabolic process0.0466783910941187
GO:0016798hydrolase activity, acting on glycosyl bonds0.0466783910941187
GO:0005773vacuole0.0466783910941187
GO:0055082cellular chemical homeostasis0.0466783910941187
GO:0006873cellular ion homeostasis0.0466783910941187
GO:0050801ion homeostasis0.0471942131820465
GO:0019318hexose metabolic process0.0471942131820465
GO:0022890inorganic cation transmembrane transporter activity0.0471942131820465
GO:0005996monosaccharide metabolic process0.0471942131820465
GO:0007610behavior0.0489368997340565
GO:0048878chemical homeostasis0.0489368997340565



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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell of uterus2.19e-126
stromal cell of endometrium2.19e-126
Disease
Ontology termp-valuen
female reproductive endometrioid cancer2.19e-126


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)
MA0003.10.00161411
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.0115261
MA0017.10.494446
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.11.27338
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.229721
MA0056.10
MA0057.10.0196406
MA0058.10.182945
MA0059.10.182001
MA0060.10.877206
MA0061.10.0537738
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.11.37852
MA0069.11.57719
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.0104193
MA0074.12.43216
MA0076.10.194691
MA0077.11.53103
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.244241
MA0089.10
MA0090.10.593146
MA0091.10.258318
MA0092.10.228476
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.141917
MA0103.10.411001
MA0105.10.074747
MA0106.10.37688
MA0107.10.0950422
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.97973
MA0122.11.73183
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.181369
MA0140.10.30631
MA0141.10.533493
MA0142.11.2271
MA0143.11.01483
MA0144.10.0838502
MA0145.10.0493052
MA0146.10.0082386
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.0512998
MA0035.20.305721
MA0039.20.192101
MA0138.20.425279
MA0002.20.0612545
MA0137.20.153033
MA0104.20.0667907
MA0047.20.366327
MA0112.20.0445156
MA0065.21.42425
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.367546
MA0155.10.11478
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.288813
MA0161.10
MA0162.10.0065085
MA0163.10.00038862
MA0164.11.03839
MA0080.20.139746
MA0018.20.378086
MA0099.20.312108
MA0079.20.00782918
MA0102.21.1957
MA0258.10.0785319
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

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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