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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0504265701716883,0.080626736260243,0,0,0.149411045406522,0.176719245822362,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.778899424047215,0.953385540195552,0.875048184635987,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.131832994540557,0,0,0,0,0,0,0,0.197604689528463,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.116105357238318,0,0,0,0,0.0834782173702644,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0477396614475454,0.0428357178336246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.269008087442184,0,0,0,0,0,0,0.387979180422312,0.129622621258172,0.568248668460832,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0878744294302742,0,0.0307366208579214,0.0527984507438095,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0932902756138882,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0734870933250891,0,0.143515142523472,0.128122390065496,0,0,0,0,0,0.114741150775265,0,0.16446763709968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.391836556644026,0.497654756499332,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0738371582016079,0,0.137404238899705,0,0,0,0,0,0,0,0,0.0483689238882358,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.207799140520579,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0468626006398675,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.516569655263704,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.235889211459974,0,0,0,0,0,0,0,0,0.420096165209593,0.288120755774485,0,0.110236269607548,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0647398703344467,0.261319173405172,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.458527296003926,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.146136648478548,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.227979188198738,0.503528998754219,0,0.256914955251363,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.342504807235995,0,0,0,0,0,0,0,0,0.555231259381818,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.497597066356314,0.0450355340939671,0,0.259094472815984,0,0.0732745932580414,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C3439_Ciliary_Lens_teratocarcinoma_liposarcoma_renal_Iris_clear|gostat_on_coexpression_clusters=GO:0001565!phorbol 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,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;2.08673,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.0107199,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3439_Ciliary_Lens_teratocarcinoma_liposarcoma_renal_Iris_clear
|gostat_on_coexpression_clusters=GO:0001565!phorbol ester receptor activity!0.00927234192864712!5583$GO:0004697!protein kinase C activity!0.00927234192864712!5583$GO:0019992!diacylglycerol binding!0.0243141410573413!5583
|id=C3439
|ontology_enrichment_celltype=CL:0000055!8.75e-18!180;CL:0002319!6.19e-13!25;CL:0000243!1.53e-12!15;CL:0000125!1.53e-12!15;CL:0000030!1.53e-12!15;CL:0000339!1.53e-12!15;CL:0000128!3.28e-12!7;CL:0000126!3.28e-12!7;CL:0000127!3.28e-12!7;CL:0002453!3.28e-12!7;CL:0000133!5.02e-11!59;CL:0000095!6.98e-11!17;CL:0000123!6.98e-11!17;CL:0000221!6.05e-09!71;CL:0002322!2.57e-08!5;CL:0000064!4.39e-07!3;CL:0005012!4.39e-07!3;CL:0000067!4.39e-07!3;CL:0002304!4.39e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002200!2.29e-10!11;UBERON:0006876!2.29e-10!11;UBERON:0000488!7.60e-09!4;UBERON:0007625!2.44e-08!11;UBERON:0001778!4.39e-07!3;UBERON:0001775!4.39e-07!3
}}

Latest revision as of 12:26, 17 September 2013


Full id: C3439_Ciliary_Lens_teratocarcinoma_liposarcoma_renal_Iris_clear



Phase1 CAGE Peaks

Hg19::chr14:61654180..61654191,+p33@PRKCH
Hg19::chr4:183006194..183006207,-p2@ENST00000505537
Hg19::chr4:183006221..183006245,-p1@ENST00000505537


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:0001565phorbol ester receptor activity0.00927234192864712
GO:0004697protein kinase C activity0.00927234192864712
GO:0019992diacylglycerol binding0.0243141410573413



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><br>

Cell Type
Ontology termp-valuen
ciliated cell5.66e-143
ciliated epithelial cell5.66e-143
multi-ciliated epithelial cell5.66e-143
non-pigmented ciliary epithelial cell5.66e-143
oligodendrocyte6.92e-147
macroglial cell6.92e-147
astrocyte6.92e-147
oligodendrocyte precursor cell6.92e-147
glial cell (sensu Vertebrata)8.74e-1415
glial cell8.74e-1415
glioblast8.74e-1415
glioblast (sensu Vertebrata)8.74e-1415
neural cell8.24e-1325
neuron associated cell3.40e-1217
neuron associated cell (sensu Vertebrata)3.40e-1217
neurectodermal cell2.59e-1159
crystallin accumulating cell5.09e-104
vertebrate lens cell5.09e-104
lens epithelial cell5.09e-104
non-terminally differentiated cell8.24e-10106
osteoblast3.08e-0911
osteoprogenitor cell3.08e-0911
mesenchyme condensation cell3.08e-0911
central nervous system pericyte6.96e-092
ectodermal cell9.56e-0972
columnar/cuboidal epithelial cell1.67e-0827
migratory neural crest cell3.25e-0741
Uber Anatomy
Ontology termp-valuen
pigment epithelium of eye3.15e-1811
atypical epithelium8.64e-184
anterior segment of eyeball4.30e-1414
ciliary epithelium5.66e-143
ciliary body5.66e-143
vasculature of organ2.32e-1311
vasculature of eye7.14e-126
uvea7.14e-126
vasculature of head7.14e-126
cuboidal epithelium5.09e-104
transparent eye structure5.09e-104
simple cuboidal epithelium5.09e-104
cranial placode5.09e-104
lens of camera-type eye5.09e-104
epithelium of lens5.09e-104
lens placode5.09e-104
lens vesicle5.09e-104
camera-type eye1.52e-0920
simple eye1.52e-0920
immature eye1.52e-0920
ocular region1.52e-0920
eyeball of camera-type eye1.52e-0920
optic cup1.52e-0920
optic vesicle1.52e-0920
eye primordium1.52e-0920
eye4.87e-0921
visual system4.87e-0921
face1.40e-0822
sense organ8.89e-0824
sensory system8.89e-0824
entire sense organ system8.89e-0824


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.12.8546
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.12.53618
MA0143.13.75836
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.12.08673
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
ESR1#2099220.51240219743630.003099741577095180.0163049060977206
NR3C1#290829.982015554115360.01278474365547170.0460295726225114



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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