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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:25, 17 September 2013


Full id: C548_Mesothelial_mesenchymal_rhabdomyosarcoma_Renal_mesothelioma_Hepatic_clear



Phase1 CAGE Peaks

Hg19::chr20:6020237..6020248,-p@chr20:6020237..6020248
-
Hg19::chr20:6020266..6020281,-p@chr20:6020266..6020281
-
Hg19::chr20:6020518..6020536,-p@chr20:6020518..6020536
-
Hg19::chr20:6022771..6022780,-p12@LRRN4
Hg19::chr20:6031540..6031548,-p@chr20:6031540..6031548
-
Hg19::chr20:6032946..6032956,-p9@AB527789
Hg19::chr20:6033494..6033509,-p5@AB527789
Hg19::chr20:6033532..6033548,-p2@AB527789
Hg19::chr20:6033667..6033675,-p13@AB527789
Hg19::chr20:6034241..6034256,-p@chr20:6034241..6034256
-
Hg19::chr20:6034557..6034560,-p10@LRRN4
Hg19::chr20:6034576..6034592,-p3@LRRN4
Hg19::chr20:6034598..6034603,-p7@LRRN4
Hg19::chr20:6034607..6034616,-p6@LRRN4
Hg19::chr20:6034618..6034669,-p1@LRRN4
Hg19::chr20:6034672..6034714,-p2@LRRN4
Hg19::chr20:6034828..6034857,-p5@LRRN4


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>

Uber Anatomy
Ontology termp-valuen
nephron tubule epithelium1.13e-4310
nephron epithelium3.02e-3515
renal tubule3.02e-3515
nephron tubule3.02e-3515
nephron3.02e-3515
uriniferous tubule3.02e-3515
nephrogenic mesenchyme3.02e-3515
excretory tube6.25e-3316
kidney epithelium6.25e-3316
kidney1.01e-3226
kidney mesenchyme1.01e-3226
upper urinary tract1.01e-3226
kidney rudiment1.01e-3226
kidney field1.01e-3226
cavitated compound organ5.17e-2731
cortex2.17e-2215
abdomen element2.69e-2254
abdominal segment element2.69e-2254
cortex of kidney1.02e-2112
renal parenchyma1.02e-2112
abdominal segment of trunk1.01e-1960
abdomen1.01e-1960
urinary system structure1.07e-1947
renal system3.16e-1948
parenchyma3.38e-1715
trunk region element1.81e-13101
compound organ1.09e-1268
abdomen connective tissue2.53e-122
abdominal segment connective tissue2.53e-122
trunk connective tissue2.53e-122
interstitial tissue2.53e-122
extraglomerular mesangium2.53e-122
kidney interstitium2.53e-122
juxtaglomerular apparatus2.53e-122
mesangium2.53e-122
subdivision of trunk9.09e-12112
renal cortex tubule1.97e-083
region of nephron tubule1.97e-083
proximal tubule1.97e-083
mesenchyme4.42e-08160
entire embryonic mesenchyme4.42e-08160
primitive nephron1.02e-077
renal glomerulus1.02e-077
renal corpuscle1.02e-077
glomerular capsule1.02e-077
metanephric mesenchyme1.02e-077
glomerular tuft1.02e-077
S-shaped body1.02e-077
renal vesicle1.02e-077
comma-shaped body1.02e-077
female gonad7.16e-0713
mesonephric epithelium8.40e-078
mesonephric tubule8.40e-078
nephric duct8.40e-078
renal duct8.40e-078
mesonephric duct8.40e-078
pronephric duct8.40e-078
Disease
Ontology termp-valuen
ovarian cancer8.59e-1414
female reproductive organ cancer3.60e-0927
reproductive organ cancer1.78e-0829


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)
MA0003.10.0481737
MA0004.10.221943
MA0006.10.112549
MA0007.10.208008
MA0009.10.621697
MA0014.10.525509
MA0017.10.425352
MA0019.10.340029
MA0024.11.30305
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.11.4832
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.12.04604
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.11.12635
MA0056.10
MA0057.10.164004
MA0058.10.153757
MA0059.10.15289
MA0060.10.0509127
MA0061.10.356644
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.0264141
MA0069.10.607975
MA0070.10.597583
MA0071.10.746772
MA0072.10.593415
MA0073.13.72477e-05
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.382364
MA0081.10.907903
MA0083.11.52135
MA0084.11.10674
MA0087.10.591148
MA0088.10.176197
MA0089.10
MA0090.10.174619
MA0091.10.636604
MA0092.10.570207
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.372085
MA0103.10.34743
MA0105.10.492971
MA0106.10.33677
MA0107.10.551112
MA0108.20.471286
MA0109.10
MA0111.10.541878
MA0113.10.924932
MA0114.10.25223
MA0115.10.850405
MA0116.10.264652
MA0117.10.656858
MA0119.10.862312
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.934169
MA0140.10.269307
MA0141.10.462123
MA0142.10.445733
MA0143.10.350722
MA0144.10.860769
MA0145.10.577453
MA0146.12.82445
MA0147.10.0784275
MA0148.10.240905
MA0149.10.261654
MA0062.20.0377014
MA0035.20.268747
MA0039.20.000794527
MA0138.20.38342
MA0002.20.174654
MA0137.20.793918
MA0104.20.0505812
MA0047.20.326636
MA0112.20.08608
MA0065.21.17085
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.280624
MA0155.11.7213
MA0156.10.4018
MA0157.10.421609
MA0158.10
MA0159.10.0787617
MA0160.12.00868
MA0161.10
MA0162.10.00317087
MA0163.10.0944046
MA0164.10.948242
MA0080.20.11444
MA0018.20.337929
MA0099.20.27482
MA0079.25.83152e-08
MA0102.21.14323
MA0258.10.218609
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
JUND#372772.880155740770420.006334289051310370.0275805392407989
STAT1#677256.090172793293880.0009955417570414920.00714397317326209



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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