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Coexpression cluster:C3475: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3475_skeletal_Mesenchymal_Alveolar_brain_Hepatic_Adipocyte_mature
|id=C3475
|ontology_enrichment_celltype=CL:0000055!3.02e-18!180;CL:0000136!7.83e-10!15;CL:0000393!6.45e-09!60;CL:0000211!6.45e-09!60;CL:0000183!7.26e-09!59;CL:0000325!9.37e-09!39;CL:0000057!1.07e-08!75;CL:0000222!1.35e-08!119;CL:0000680!1.44e-07!57;CL:0000056!1.44e-07!57;CL:0000355!1.44e-07!57;CL:0000187!1.55e-07!54
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!9.60e-18!365;UBERON:0003075!6.95e-17!86;UBERON:0007284!6.95e-17!86;UBERON:0002346!2.96e-16!90;UBERON:0000119!3.54e-16!312;UBERON:0000483!2.18e-15!309;UBERON:0003056!1.69e-13!61;UBERON:0000468!2.09e-13!659;UBERON:0005743!3.11e-13!86;UBERON:0000033!3.15e-12!123;UBERON:0001017!5.38e-12!82;UBERON:0000073!7.18e-12!94;UBERON:0001016!7.18e-12!94;UBERON:0000153!9.99e-12!129;UBERON:0007811!9.99e-12!129;UBERON:0004121!1.35e-11!169;UBERON:0000924!2.12e-11!173;UBERON:0006601!2.12e-11!173;UBERON:0000025!3.42e-11!194;UBERON:0001049!1.38e-10!57;UBERON:0005068!1.38e-10!57;UBERON:0006241!1.38e-10!57;UBERON:0007135!1.38e-10!57;UBERON:0002616!1.66e-10!59;UBERON:0007023!1.96e-10!115;UBERON:0000481!2.02e-10!347;UBERON:0004111!1.01e-09!241;UBERON:0000477!1.88e-09!286;UBERON:0000467!2.26e-09!625;UBERON:0000480!3.82e-09!626;UBERON:0000064!4.37e-09!219;UBERON:0000955!4.95e-09!69;UBERON:0006238!4.95e-09!69;UBERON:0003080!1.75e-08!42;UBERON:0000922!1.98e-08!612;UBERON:0002780!2.34e-08!41;UBERON:0001890!2.34e-08!41;UBERON:0006240!2.34e-08!41;UBERON:0002385!2.51e-08!63;UBERON:0001015!2.51e-08!63;UBERON:0000383!2.51e-08!63;UBERON:0000914!2.75e-08!83;UBERON:0002329!2.75e-08!83;UBERON:0003077!2.75e-08!83;UBERON:0003059!2.75e-08!83;UBERON:0007282!2.75e-08!83;UBERON:0009618!2.75e-08!83;UBERON:0007285!2.75e-08!83;UBERON:0001134!3.65e-08!61;UBERON:0002036!3.65e-08!61;UBERON:0003082!3.65e-08!61;UBERON:0005256!1.21e-07!143;UBERON:0002050!1.42e-07!605;UBERON:0005423!1.42e-07!605;UBERON:0004290!1.99e-07!70;UBERON:0001013!2.13e-07!14;UBERON:0000923!2.72e-07!604;UBERON:0005291!2.72e-07!604;UBERON:0006598!2.72e-07!604;UBERON:0002532!2.72e-07!604;UBERON:0002104!2.96e-07!21;UBERON:0001893!4.36e-07!34;UBERON:0001869!4.46e-07!32;UBERON:0000486!4.53e-07!82;UBERON:0001032!5.85e-07!24;UBERON:0004456!5.85e-07!24;UBERON:0002020!6.55e-07!34;UBERON:0003528!6.55e-07!34;UBERON:0000970!6.97e-07!20;UBERON:0002049!7.86e-07!79;UBERON:0007798!7.86e-07!79;UBERON:0002791!8.18e-07!33
}}

Latest revision as of 12:27, 17 September 2013


Full id: C3475_skeletal_Mesenchymal_Alveolar_brain_Hepatic_Adipocyte_mature



Phase1 CAGE Peaks

Hg19::chr15:23932389..23932401,-p3@NDN
Hg19::chr15:23932412..23932434,-p2@NDN
Hg19::chr15:23932437..23932459,-p1@NDN


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
fat cell5.15e-1015
non-terminally differentiated cell1.47e-09106
mesodermal cell7.22e-09121
fibroblast9.01e-0976
electrically responsive cell1.34e-0861
electrically active cell1.34e-0861
contractile cell1.39e-0859
muscle cell2.87e-0755
muscle precursor cell3.16e-0758
myoblast3.16e-0758
multi-potent skeletal muscle stem cell3.16e-0758
Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest2.99e-18132
neural plate1.03e-1782
presumptive neural plate1.03e-1782
neurectoderm7.11e-1786
cell layer4.12e-15309
epithelium2.52e-14306
pre-chordal neural plate3.60e-1461
anatomical cluster7.28e-14373
multi-tissue structure2.22e-13342
multi-cellular organism1.00e-12656
central nervous system1.53e-1281
nervous system2.72e-1189
ecto-epithelium4.55e-11104
neural tube5.47e-1156
neural rod5.47e-1156
future spinal cord5.47e-1156
neural keel5.47e-1156
ectoderm-derived structure8.07e-11171
ectoderm8.07e-11171
presumptive ectoderm8.07e-11171
regional part of nervous system1.30e-1053
regional part of brain1.30e-1053
tube1.77e-10192
adult organism1.94e-10114
organ part1.69e-09218
brain1.82e-0968
future brain1.82e-0968
anatomical conduit2.06e-09240
anatomical system4.26e-09624
anatomical group6.76e-09625
regional part of forebrain1.02e-0841
forebrain1.02e-0841
anterior neural tube1.02e-0841
future forebrain1.02e-0841
epithelial vesicle1.64e-0878
embryonic structure2.91e-08564
embryo3.66e-08592
developing anatomical structure4.63e-08581
muscle tissue5.84e-0864
musculature5.84e-0864
musculature of body5.84e-0864
germ layer8.17e-08560
germ layer / neural crest8.17e-08560
embryonic tissue8.17e-08560
presumptive structure8.17e-08560
germ layer / neural crest derived structure8.17e-08560
epiblast (generic)8.17e-08560
skeletal muscle tissue8.35e-0862
striated muscle tissue8.35e-0862
myotome8.35e-0862
adipose tissue1.44e-0714
dense mesenchyme tissue2.04e-0773
cerebral hemisphere2.85e-0732
eye2.87e-0721
visual system2.87e-0721
paraxial mesoderm2.89e-0772
presumptive paraxial mesoderm2.89e-0772
telencephalon2.95e-0734
brain grey matter3.98e-0734
gray matter3.98e-0734
sense organ5.28e-0724
sensory system5.28e-0724
entire sense organ system5.28e-0724
somite5.49e-0771
presomitic mesoderm5.49e-0771
presumptive segmental plate5.49e-0771
dermomyotome5.49e-0771
trunk paraxial mesoderm5.49e-0771
camera-type eye6.77e-0720
simple eye6.77e-0720
immature eye6.77e-0720
ocular region6.77e-0720
eyeball of camera-type eye6.77e-0720
optic cup6.77e-0720
optic vesicle6.77e-0720
eye primordium6.77e-0720
regional part of telencephalon7.40e-0732
face8.06e-0722


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.12.63873
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.12.34614
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
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
MA0139.11.12079
MA0140.10.894983
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.13.73313
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.12.48891
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
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
E2F6#187635.017155731697390.00791769806886330.0321357247246236
NRF1#4899312.21027944771090.0005492172401020010.00470354238122287
SPI1#668838.204323508522730.001810593189410520.0108951683630356



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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