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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0724992894770213

Latest revision as of 11:33, 17 September 2013


Full id: C893_osteoclastoma_Urothelial_tubular_nonsmall_Mesenchymal_Renal_hepatic



Phase1 CAGE Peaks

Hg19::chr12:47473475..47473484,-p9@AMIGO2
Hg19::chr12:47473520..47473544,-p3@AMIGO2
Hg19::chr12:47473557..47473568,-p8@AMIGO2
Hg19::chr12:47473642..47473653,-p7@AMIGO2
Hg19::chr12:47473707..47473757,-p1@AMIGO2
Hg19::chr12:47473898..47473903,-p11@AMIGO2
Hg19::chr12:47473904..47473917,-p6@AMIGO2
Hg19::chr12:47473920..47473939,-p5@AMIGO2
Hg19::chr12:47474192..47474251,-p4@AMIGO2


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell1.31e-12253
endo-epithelial cell1.38e-1142
endodermal cell6.61e-0858
embryonic cell1.09e-07250
kidney tubule cell4.43e-0710
nephron tubule epithelial cell4.43e-0710
Uber Anatomy
Ontology termp-valuen
trunk2.37e-13199
organism subdivision2.96e-13264
anatomical space9.26e-0995
subdivision of trunk1.72e-08112
immaterial anatomical entity4.50e-08117
female organism4.80e-0841
body cavity precursor8.96e-0854
multi-tissue structure1.19e-07342
epithelial bud1.65e-0737
endo-epithelium3.20e-0782
body cavity4.12e-0746
cell layer4.41e-07309
nephron tubule epithelium4.43e-0710
epithelial tube5.15e-07117
reproductive structure5.91e-0759
reproductive system5.91e-0759
epithelial fold8.62e-0747
renal system9.24e-0748
female reproductive organ9.85e-0737
female reproductive system9.85e-0737
Disease
Ontology termp-valuen
female reproductive organ cancer2.59e-1127
reproductive organ cancer9.75e-1129
ovarian cancer1.44e-0714


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)
MA0003.17.76058
MA0004.10.415381
MA0006.10.733408
MA0007.10.397529
MA0009.10.870971
MA0014.13.27412
MA0017.15.08432
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
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
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.11.55919
MA0060.12.88716
MA0061.12.66787
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.11.21679
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.865814
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.11.36936
MA0103.10.257174
MA0105.15.90412
MA0106.10.554855
MA0107.13.28039
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.15.0101
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.12.25779
MA0130.10
MA0131.12.56981
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.12.56675
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.11.0529
MA0145.10.706237
MA0146.11.3662
MA0147.11.14329
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.22.14461
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.21.50683
MA0047.20.542971
MA0112.20.378721
MA0065.23.91739
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.225151
MA0155.11.00468
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.11.15068
MA0161.10
MA0162.10.0533066
MA0163.10.384654
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.22.0981
MA0079.28.0379
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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
CEBPB#105176.199781486752641.39459740509258e-050.000336530402935453
E2F6#187684.459693983731011.843503537119e-050.000419006889908969
FOXA1#316944.925075444171310.005758150542003090.0259291805482801
GABPB1#255353.926491020101210.004337976092287310.0205849373030303
GTF2F1#296279.908625126367065.7263614460198e-072.63925623592614e-05
NR3C1#290858.318346295096130.0001331418467233980.00174886194566029
POLR2A#543092.147453176558070.001029412892608020.00728541391143792
ZBTB7A#5134197.35190930787591.59170049418346e-081.16411490134473e-06



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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