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{{Coexpression_clusters
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.32578,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;1.38179,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2112_Smooth_Amniotic_mesenchymal_Myoblast_Fibroblast_Lens_cerebellum
|id=C2112
|ontology_enrichment_celltype=CL:0000055!3.36e-32!180;CL:0000057!3.64e-17!75;CL:0000680!7.22e-16!57;CL:0000056!7.22e-16!57;CL:0000355!7.22e-16!57;CL:0000183!5.68e-15!59;CL:0000359!6.24e-15!32;CL:0000187!1.02e-14!54;CL:0000192!2.86e-14!42;CL:0000514!2.86e-14!42;CL:0000393!7.51e-13!60;CL:0000211!7.51e-13!60;CL:0000220!4.26e-08!246;CL:0002321!4.88e-08!248;CL:0002620!2.51e-07!23
|ontology_enrichment_disease=DOID:2394!8.16e-08!14
|ontology_enrichment_uberon=UBERON:0000475!2.95e-26!365;UBERON:0000914!1.71e-23!83;UBERON:0002329!1.71e-23!83;UBERON:0003077!1.71e-23!83;UBERON:0003059!1.71e-23!83;UBERON:0007282!1.71e-23!83;UBERON:0009618!1.71e-23!83;UBERON:0007285!1.71e-23!83;UBERON:0000119!8.55e-23!312;UBERON:0000483!5.90e-22!309;UBERON:0000486!2.42e-20!82;UBERON:0000481!1.75e-18!347;UBERON:0004290!1.99e-18!70;UBERON:0001134!5.74e-16!61;UBERON:0002036!5.74e-16!61;UBERON:0003082!5.74e-16!61;UBERON:0002385!1.01e-15!63;UBERON:0001015!1.01e-15!63;UBERON:0000383!1.01e-15!63;UBERON:0000033!1.59e-15!123;UBERON:0005256!6.40e-15!143;UBERON:0000468!7.78e-15!659;UBERON:0000153!1.03e-14!129;UBERON:0007811!1.03e-14!129;UBERON:0000924!1.05e-14!173;UBERON:0006601!1.05e-14!173;UBERON:0004121!4.07e-14!169;UBERON:0000467!6.15e-14!625;UBERON:0000480!1.01e-13!626;UBERON:0000477!2.98e-13!286;UBERON:0001637!1.48e-12!42;UBERON:0003509!1.48e-12!42;UBERON:0004572!1.48e-12!42;UBERON:0004872!1.58e-12!84;UBERON:0004111!5.70e-12!241;UBERON:0000025!1.32e-11!194;UBERON:0002049!2.19e-11!79;UBERON:0007798!2.19e-11!79;UBERON:0001981!3.71e-11!60;UBERON:0007500!3.71e-11!60;UBERON:0004537!3.71e-11!60;UBERON:0006965!3.71e-11!60;UBERON:0000922!8.33e-11!612;UBERON:0003102!1.10e-10!95;UBERON:0002050!1.24e-10!605;UBERON:0005423!1.24e-10!605;UBERON:0000923!1.46e-10!604;UBERON:0005291!1.46e-10!604;UBERON:0006598!1.46e-10!604;UBERON:0002532!1.46e-10!604;UBERON:0004573!5.39e-10!33;UBERON:0004571!5.39e-10!33;UBERON:0002346!9.09e-10!90;UBERON:0000055!3.02e-09!69;UBERON:0003075!3.09e-09!86;UBERON:0007284!3.09e-09!86;UBERON:0000955!3.97e-09!69;UBERON:0006238!3.97e-09!69;UBERON:0002616!5.08e-09!59;UBERON:0002097!1.25e-08!40;UBERON:0005743!2.77e-08!86;UBERON:0001017!3.43e-08!82;UBERON:0000479!4.05e-08!787;UBERON:0001049!5.05e-08!57;UBERON:0005068!5.05e-08!57;UBERON:0006241!5.05e-08!57;UBERON:0007135!5.05e-08!57;UBERON:0002199!5.49e-08!45;UBERON:0002416!5.49e-08!45;UBERON:0000064!6.75e-08!219;UBERON:0002100!7.48e-08!216;UBERON:0003914!7.61e-08!118;UBERON:0000073!7.72e-08!94;UBERON:0001016!7.72e-08!94;UBERON:0004535!7.95e-08!110;UBERON:0000490!1.00e-07!138;UBERON:0001009!1.34e-07!113;UBERON:0001869!1.46e-07!32;UBERON:0003056!1.67e-07!61;UBERON:0001893!1.96e-07!34;UBERON:0000956!2.34e-07!25;UBERON:0000203!2.34e-07!25;UBERON:0002020!3.35e-07!34;UBERON:0003528!3.35e-07!34;UBERON:0002791!4.25e-07!33;UBERON:0002619!7.58e-07!22;UBERON:0003129!7.67e-07!11;UBERON:0001950!8.31e-07!20
}}

Latest revision as of 11:59, 17 September 2013


Full id: C2112_Smooth_Amniotic_mesenchymal_Myoblast_Fibroblast_Lens_cerebellum



Phase1 CAGE Peaks

Hg19::chr11:131781197..131781214,+p14@NTM
Hg19::chr11:131781224..131781254,+p5@NTM
Hg19::chr11:131781256..131781281,+p11@NTM
Hg19::chr11:131781290..131781355,+p2@NTM


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
cell layer9.62e-23309
epithelium4.56e-22306
multilaminar epithelium6.66e-2283
dense mesenchyme tissue2.21e-2073
paraxial mesoderm6.76e-2072
presumptive paraxial mesoderm6.76e-2072
somite1.49e-1971
presomitic mesoderm1.49e-1971
presumptive segmental plate1.49e-1971
dermomyotome1.49e-1971
trunk paraxial mesoderm1.49e-1971
multi-tissue structure1.65e-18342
epithelial vesicle2.88e-1878
structure with developmental contribution from neural crest3.79e-18132
skeletal muscle tissue1.08e-1662
striated muscle tissue1.08e-1662
myotome1.08e-1662
muscle tissue4.79e-1664
musculature4.79e-1664
musculature of body4.79e-1664
ectoderm-derived structure2.63e-14171
ectoderm2.63e-14171
presumptive ectoderm2.63e-14171
ecto-epithelium1.59e-13104
multi-cellular organism4.57e-13656
anatomical system7.99e-13624
anatomical group1.17e-12625
anatomical cluster3.09e-12373
artery8.23e-1242
arterial blood vessel8.23e-1242
arterial system8.23e-1242
surface structure3.60e-1199
neurectoderm5.34e-1186
tube1.36e-10192
anatomical conduit1.60e-10240
neural plate1.88e-1082
presumptive neural plate1.88e-1082
embryonic structure2.73e-10564
developing anatomical structure2.98e-10581
brain4.39e-1068
future brain4.39e-1068
trunk mesenchyme5.99e-10122
systemic artery7.61e-1033
systemic arterial system7.61e-1033
regional part of nervous system7.80e-1053
regional part of brain7.80e-1053
embryo1.00e-09592
germ layer1.98e-09560
germ layer / neural crest1.98e-09560
embryonic tissue1.98e-09560
presumptive structure1.98e-09560
germ layer / neural crest derived structure1.98e-09560
epiblast (generic)1.98e-09560
splanchnic layer of lateral plate mesoderm2.46e-0983
organism subdivision2.82e-09264
unilaminar epithelium3.46e-09148
neural tube4.88e-0956
neural rod4.88e-0956
future spinal cord4.88e-0956
neural keel4.88e-0956
vasculature9.34e-0978
vascular system9.34e-0978
epithelial tube open at both ends1.03e-0859
blood vessel1.03e-0859
blood vasculature1.03e-0859
vascular cord1.03e-0859
cerebral hemisphere2.25e-0832
telencephalon2.43e-0834
cerebral cortex2.90e-0825
pallium2.90e-0825
central nervous system3.39e-0881
skin of body4.16e-0841
brain grey matter4.74e-0834
gray matter4.74e-0834
mesenchyme5.48e-08160
entire embryonic mesenchyme5.48e-08160
tissue5.65e-08773
regional part of telencephalon7.15e-0832
integument9.13e-0846
integumental system9.13e-0846
regional part of cerebral cortex1.05e-0722
neocortex1.13e-0720
pre-chordal neural plate1.72e-0761
nervous system1.79e-0789
blood vessel smooth muscle2.48e-0710
arterial system smooth muscle2.48e-0710

Disease
Ontology termp-valuen


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)
MA0003.11.05935
MA0004.10.71247
MA0006.10.532262
MA0007.12.78189
MA0009.11.20602
MA0014.10.0695829
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.12.66951
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.24.47016
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.13.14178
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
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
CTCF#1066445.360256373075030.001211145381643620.00815596186172405



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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