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

Latest revision as of 11:42, 17 September 2013


Full id: C1318_retina_Melanocyte_globus_caudate_eye_melanoma_nucleus



Phase1 CAGE Peaks

Hg19::chr10:63123003..63123038,-p@chr10:63123003..63123038
-
Hg19::chr3:69986115..69986119,+p12@MITF
Hg19::chr4:22341289..22341308,-p1@LOC100505912
Hg19::chr6:10412249..10412254,-p41@TFAP2A
Hg19::chr6:10412262..10412271,-p21@TFAP2A
Hg19::chr7:116311841..116311852,+p33@MET


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

p.valueFDRnGenesnPathwayName
1.82684577066052e-050.0115639337282811271Melanoma (KEGG):05218



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:0048012hepatocyte growth factor receptor signaling pathway0.00435652890615801
GO:0005008hepatocyte growth factor receptor activity0.00435652890615801
GO:0051450myoblast proliferation0.00435652890615801
GO:0016563transcription activator activity0.00909867646707665
GO:0007275multicellular organismal development0.00916255739815988
GO:0030318melanocyte differentiation0.014933592894531
GO:0050931pigment cell differentiation0.014933592894531
GO:0032502developmental process0.0175503814073968
GO:0045178basal part of cell0.0175503814073968
GO:0048066pigmentation during development0.0175503814073968
GO:0009925basal plasma membrane0.0175503814073968
GO:0032501multicellular organismal process0.0175503814073968
GO:0030317sperm motility0.0195928403967735
GO:0007595lactation0.0195928403967735
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0220380517978679
GO:0030534adult behavior0.0220380517978679
GO:0019861flagellum0.0257497172747369
GO:0001764neuron migration0.0257497172747369
GO:0048513organ development0.0257497172747369
GO:0046777protein amino acid autophosphorylation0.0285907117347742
GO:0016540protein autoprocessing0.0285907117347742
GO:0000187activation of MAPK activity0.0331598958932373
GO:0048609reproductive process in a multicellular organism0.0331598958932373
GO:0032504multicellular organism reproduction0.0331598958932373
GO:0043406positive regulation of MAP kinase activity0.0344377311136857
GO:0048731system development0.036895850629173
GO:0016323basolateral plasma membrane0.0391939630078132
GO:0065007biological regulation0.0391939630078132
GO:0043405regulation of MAP kinase activity0.0391939630078132
GO:0048869cellular developmental process0.0391939630078132
GO:0030154cell differentiation0.0391939630078132
GO:0016485protein processing0.0403175002874271
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0430321421924296
GO:0048856anatomical structure development0.0436787634291092
GO:0019199transmembrane receptor protein kinase activity0.0443602688604381
GO:0050954sensory perception of mechanical stimulus0.0443602688604381
GO:0007605sensory perception of sound0.0443602688604381
GO:0007420brain development0.0443602688604381
GO:0045860positive regulation of protein kinase activity0.0443602688604381
GO:0033674positive regulation of kinase activity0.0443602688604381
GO:0043283biopolymer metabolic process0.0443602688604381
GO:0007398ectoderm development0.0443602688604381
GO:0051347positive regulation of transferase activity0.0443602688604381
GO:0000165MAPKKK cascade0.0443602688604381
GO:0007517muscle development0.0497038261938837



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
melanocyte1.18e-4410
melanoblast1.18e-4410
pigment cell9.91e-3214
neurecto-epithelial cell1.39e-2820
columnar/cuboidal epithelial cell6.25e-2127
ecto-epithelial cell2.02e-1634
light melanocyte1.70e-133
migratory neural crest cell9.83e-1341
neurectodermal cell5.81e-1159
dark melanocyte7.40e-111
ectodermal cell8.20e-0972
Uber Anatomy
Ontology termp-valuen
substantia nigra1.73e-101
midbrain nucleus1.73e-101
regional part of midbrain1.73e-101
midbrain1.73e-101
presumptive midbrain1.73e-101
midbrain neural tube1.73e-101
dura mater4.33e-101
future meninx4.33e-101
ectomeninx4.33e-101
future dura mater4.33e-101
insula4.75e-101
Disease
Ontology termp-valuen
melanoma1.97e-192


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.11.59836
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.11.34656
MA0051.11.58921
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.13.81132
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.11.12205
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.11.72302
MA0144.10.811435
MA0145.10.107156
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.21.06611
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.000444266
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
CTBP2#1488220.9056667797760.003653095132163690.0184499058227208
SUZ12#23512216.70526030368760.005660234682079570.0255565799127451



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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