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Coexpression cluster:C2746: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2746_mature_breast_colon_uterus_vagina_hippocampus_smooth
|id=C2746
|ontology_enrichment_celltype=CL:0000055!2.84e-15!180;CL:0000680!3.68e-08!57;CL:0000056!3.68e-08!57;CL:0000355!3.68e-08!57;CL:0000136!3.87e-08!15;CL:0000187!6.06e-08!54;CL:0000183!9.54e-08!59;CL:0000057!2.17e-07!75;CL:0000393!8.16e-07!60;CL:0000211!8.16e-07!60
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!9.84e-33!365;UBERON:0000119!6.04e-26!312;UBERON:0007023!7.84e-26!115;UBERON:0000033!8.01e-26!123;UBERON:0000955!1.14e-25!69;UBERON:0006238!1.14e-25!69;UBERON:0000483!1.43e-25!309;UBERON:0003075!5.24e-25!86;UBERON:0007284!5.24e-25!86;UBERON:0001017!5.93e-25!82;UBERON:0000153!7.55e-25!129;UBERON:0007811!7.55e-25!129;UBERON:0004121!8.24e-25!169;UBERON:0000481!1.00e-24!347;UBERON:0005743!1.02e-24!86;UBERON:0002616!8.63e-24!59;UBERON:0001049!3.22e-23!57;UBERON:0005068!3.22e-23!57;UBERON:0006241!3.22e-23!57;UBERON:0007135!3.22e-23!57;UBERON:0000924!5.31e-23!173;UBERON:0006601!5.31e-23!173;UBERON:0002346!2.89e-22!90;UBERON:0000073!4.63e-21!94;UBERON:0001016!4.63e-21!94;UBERON:0003056!3.74e-20!61;UBERON:0003080!3.83e-20!42;UBERON:0000468!1.24e-19!659;UBERON:0002780!1.87e-19!41;UBERON:0001890!1.87e-19!41;UBERON:0006240!1.87e-19!41;UBERON:0000477!3.07e-19!286;UBERON:0004111!3.95e-19!241;UBERON:0000025!2.77e-17!194;UBERON:0002020!3.82e-17!34;UBERON:0003528!3.82e-17!34;UBERON:0001893!8.60e-17!34;UBERON:0001869!1.00e-16!32;UBERON:0002791!3.18e-16!33;UBERON:0000467!8.14e-16!625;UBERON:0000480!1.53e-15!626;UBERON:0000922!3.90e-14!612;UBERON:0002050!1.01e-13!605;UBERON:0005423!1.01e-13!605;UBERON:0000956!1.88e-13!25;UBERON:0000203!1.88e-13!25;UBERON:0000923!2.45e-13!604;UBERON:0005291!2.45e-13!604;UBERON:0006598!2.45e-13!604;UBERON:0002532!2.45e-13!604;UBERON:0002619!1.27e-12!22;UBERON:0000914!8.37e-12!83;UBERON:0002329!8.37e-12!83;UBERON:0003077!8.37e-12!83;UBERON:0003059!8.37e-12!83;UBERON:0007282!8.37e-12!83;UBERON:0009618!8.37e-12!83;UBERON:0007285!8.37e-12!83;UBERON:0000062!1.83e-11!511;UBERON:0001950!2.48e-11!20;UBERON:0000064!1.35e-10!219;UBERON:0005256!1.80e-10!143;UBERON:0004290!2.41e-10!70;UBERON:0002385!1.69e-09!63;UBERON:0001015!1.69e-09!63;UBERON:0000383!1.69e-09!63;UBERON:0000486!1.70e-09!82;UBERON:0000479!3.78e-09!787;UBERON:0001134!6.24e-09!61;UBERON:0002036!6.24e-09!61;UBERON:0003082!6.24e-09!61;UBERON:0002100!1.22e-07!216
}}

Latest revision as of 12:12, 17 September 2013


Full id: C2746_mature_breast_colon_uterus_vagina_hippocampus_smooth



Phase1 CAGE Peaks

Hg19::chr3:64253787..64253799,-p5@PRICKLE2
Hg19::chr3:64253805..64253834,-p2@PRICKLE2
Hg19::chr3:64253837..64253863,-p1@PRICKLE2
Hg19::chr3:64253867..64253883,-p3@PRICKLE2


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><br>

Cell Type
Ontology termp-valuen
contractile cell6.87e-0859
muscle cell1.12e-0755
non-terminally differentiated cell1.19e-07106
muscle precursor cell1.20e-0758
myoblast1.20e-0758
multi-potent skeletal muscle stem cell1.20e-0758
fat cell2.75e-0715
fibroblast4.08e-0776
Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest3.03e-30132
multi-tissue structure8.68e-30342
adult organism1.80e-26114
brain6.89e-2668
future brain6.89e-2668
cell layer1.21e-25309
epithelium3.69e-25306
ecto-epithelium3.98e-25104
neural plate5.98e-2582
presumptive neural plate5.98e-2582
central nervous system6.18e-2581
ectoderm-derived structure7.04e-25171
ectoderm7.04e-25171
presumptive ectoderm7.04e-25171
anatomical cluster7.05e-25373
neural tube2.54e-2356
neural rod2.54e-2356
future spinal cord2.54e-2356
neural keel2.54e-2356
regional part of nervous system2.02e-2253
regional part of brain2.02e-2253
neurectoderm3.73e-2286
nervous system4.97e-2189
regional part of forebrain1.46e-2041
forebrain1.46e-2041
anterior neural tube1.46e-2041
future forebrain1.46e-2041
multi-cellular organism2.42e-20656
pre-chordal neural plate3.73e-2061
anatomical conduit1.07e-18240
brain grey matter9.94e-1834
gray matter9.94e-1834
telencephalon1.88e-1734
cerebral hemisphere2.34e-1732
embryonic structure4.04e-17564
regional part of telencephalon6.80e-1732
developing anatomical structure8.07e-17581
tube9.01e-17192
anatomical system2.67e-16624
embryo3.03e-16592
anatomical group4.96e-16625
germ layer6.81e-16560
germ layer / neural crest6.81e-16560
embryonic tissue6.81e-16560
presumptive structure6.81e-16560
germ layer / neural crest derived structure6.81e-16560
epiblast (generic)6.81e-16560
organ system subdivision4.29e-15223
cerebral cortex3.92e-1425
pallium3.92e-1425
regional part of cerebral cortex2.51e-1322
neocortex4.59e-1220
tissue1.68e-11773
organ3.02e-11503
organ part8.89e-11218
paraxial mesoderm2.15e-1072
presumptive paraxial mesoderm2.15e-1072
dense mesenchyme tissue2.44e-1073
somite6.17e-1071
presomitic mesoderm6.17e-1071
presumptive segmental plate6.17e-1071
dermomyotome6.17e-1071
trunk paraxial mesoderm6.17e-1071
mesenchyme7.71e-10160
entire embryonic mesenchyme7.71e-10160
organism subdivision1.38e-09264
multilaminar epithelium2.55e-0983
epithelial vesicle4.19e-0978
muscle tissue5.51e-0964
musculature5.51e-0964
musculature of body5.51e-0964
trunk mesenchyme1.37e-08122
skeletal muscle tissue1.72e-0862
striated muscle tissue1.72e-0862
myotome1.72e-0862


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.14.64626
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.12.526
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.380957
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.13.80961
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.11.9583
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.12.01976
MA0117.11.24497
MA0119.10.586221
MA0122.12.8366
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.11.70272
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.12.59564
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.10.309472
MA0163.12.49771
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
NANOG#79923429.24477848101271.36586687657858e-065.34669305558436e-05
TAF1#687243.343046285745290.008005664898701650.0322894738686762



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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