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{{Coexpression_clusters
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|full_id=C4026_pineal_Mesenchymal_brain_Cardiac_amygdala_occipital_hippocampus
|id=C4026
|ontology_enrichment_celltype=CL:0000055!3.77e-09!180;CL:0000222!5.88e-08!119;CL:0000183!4.55e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!6.55e-29!57;UBERON:0005068!6.55e-29!57;UBERON:0006241!6.55e-29!57;UBERON:0007135!6.55e-29!57;UBERON:0002616!3.34e-27!59;UBERON:0001017!4.44e-26!82;UBERON:0005743!1.27e-25!86;UBERON:0000955!6.24e-25!69;UBERON:0006238!6.24e-25!69;UBERON:0002346!1.87e-24!90;UBERON:0007023!4.45e-24!115;UBERON:0003075!5.10e-24!86;UBERON:0007284!5.10e-24!86;UBERON:0000073!6.71e-24!94;UBERON:0001016!6.71e-24!94;UBERON:0000025!1.67e-23!194;UBERON:0003080!2.96e-21!42;UBERON:0002780!6.48e-21!41;UBERON:0001890!6.48e-21!41;UBERON:0006240!6.48e-21!41;UBERON:0004111!2.01e-20!241;UBERON:0002020!1.69e-18!34;UBERON:0003528!1.69e-18!34;UBERON:0001893!4.39e-18!34;UBERON:0000475!1.07e-17!365;UBERON:0002791!1.48e-17!33;UBERON:0001869!2.39e-17!32;UBERON:0000924!3.62e-17!173;UBERON:0006601!3.62e-17!173;UBERON:0004121!1.33e-16!169;UBERON:0000483!1.36e-16!309;UBERON:0000119!1.47e-16!312;UBERON:0000477!1.48e-16!286;UBERON:0000033!1.10e-15!123;UBERON:0003056!3.41e-15!61;UBERON:0000468!6.41e-15!659;UBERON:0002619!1.01e-14!22;UBERON:0000153!1.30e-14!129;UBERON:0007811!1.30e-14!129;UBERON:0000956!9.57e-14!25;UBERON:0000203!9.57e-14!25;UBERON:0001950!1.72e-13!20;UBERON:0000467!2.84e-12!625;UBERON:0000480!5.10e-12!626;UBERON:0000922!5.27e-10!612;UBERON:0000481!6.10e-10!347;UBERON:0002050!6.23e-10!605;UBERON:0005423!6.23e-10!605;UBERON:0000923!1.20e-09!604;UBERON:0005291!1.20e-09!604;UBERON:0006598!1.20e-09!604;UBERON:0002532!1.20e-09!604;UBERON:0004872!7.24e-09!84;UBERON:0003076!8.95e-09!15;UBERON:0003057!8.95e-09!15;UBERON:0002049!1.11e-08!79;UBERON:0007798!1.11e-08!79;UBERON:0000055!3.44e-08!69;UBERON:0004732!5.81e-08!13;UBERON:0003914!6.57e-08!118;UBERON:0001981!1.33e-07!60;UBERON:0007500!1.33e-07!60;UBERON:0004537!1.33e-07!60;UBERON:0006965!1.33e-07!60;UBERON:0001009!2.11e-07!113;UBERON:0004733!2.42e-07!12;UBERON:0002028!2.42e-07!12;UBERON:0007277!2.42e-07!12;UBERON:0005256!5.20e-07!143;UBERON:0000914!9.41e-07!83;UBERON:0002329!9.41e-07!83;UBERON:0003077!9.41e-07!83;UBERON:0003059!9.41e-07!83;UBERON:0007282!9.41e-07!83;UBERON:0009618!9.41e-07!83;UBERON:0007285!9.41e-07!83
}}

Latest revision as of 12:37, 17 September 2013


Full id: C4026_pineal_Mesenchymal_brain_Cardiac_amygdala_occipital_hippocampus



Phase1 CAGE Peaks

Hg19::chr20:33146490..33146508,+p3@MAP1LC3A
Hg19::chr20:33146510..33146549,+p1@MAP1LC3A
Hg19::chr20:33146551..33146567,+p2@MAP1LC3A


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
mesodermal cell9.08e-09121
non-terminally differentiated cell5.97e-08106
contractile cell1.08e-0759
electrically responsive cell7.94e-0761
electrically active cell7.94e-0761
Uber Anatomy
Ontology termp-valuen
neural tube4.95e-2756
neural rod4.95e-2756
future spinal cord4.95e-2756
neural keel4.95e-2756
regional part of nervous system1.07e-2553
regional part of brain1.07e-2553
central nervous system1.12e-2481
brain1.09e-2368
future brain1.09e-2368
structure with developmental contribution from neural crest3.01e-23132
neurectoderm4.70e-2386
nervous system8.06e-2389
tube1.30e-22192
neural plate1.30e-2282
presumptive neural plate1.30e-2282
adult organism1.31e-22114
anatomical conduit4.63e-20240
regional part of forebrain5.46e-2041
forebrain5.46e-2041
anterior neural tube5.46e-2041
future forebrain5.46e-2041
ecto-epithelium5.09e-18104
brain grey matter6.74e-1834
gray matter6.74e-1834
telencephalon1.92e-1734
cerebral hemisphere5.66e-1732
regional part of telencephalon1.01e-1632
epithelium1.54e-16306
cell layer1.55e-16309
ectoderm-derived structure2.65e-16171
ectoderm2.65e-16171
presumptive ectoderm2.65e-16171
multi-cellular organism2.89e-16656
anatomical cluster9.96e-16373
pre-chordal neural plate1.38e-1461
regional part of cerebral cortex2.13e-1422
anatomical system5.16e-14624
anatomical group9.37e-14625
cerebral cortex1.75e-1325
pallium1.75e-1325
neocortex3.22e-1320
multi-tissue structure3.64e-12342
embryonic structure5.12e-10564
germ layer6.91e-10560
germ layer / neural crest6.91e-10560
embryonic tissue6.91e-10560
presumptive structure6.91e-10560
germ layer / neural crest derived structure6.91e-10560
epiblast (generic)6.91e-10560
embryo7.37e-10592
developing anatomical structure1.42e-09581
splanchnic layer of lateral plate mesoderm4.33e-0983
vasculature1.20e-0878
vascular system1.20e-0878
epithelial vesicle1.51e-0878
vessel2.90e-0868
posterior neural tube3.35e-0815
chordal neural plate3.35e-0815
epithelial tube3.90e-08117
dense mesenchyme tissue1.04e-0773
circulatory system1.17e-07112
epithelial tube open at both ends1.27e-0759
blood vessel1.27e-0759
blood vasculature1.27e-0759
vascular cord1.27e-0759
segmental subdivision of nervous system1.34e-0713
mesenchyme1.64e-07160
entire embryonic mesenchyme1.64e-07160
paraxial mesoderm1.78e-0772
presumptive paraxial mesoderm1.78e-0772
somite4.37e-0771
presomitic mesoderm4.37e-0771
presumptive segmental plate4.37e-0771
dermomyotome4.37e-0771
trunk paraxial mesoderm4.37e-0771
muscle tissue5.08e-0764
musculature5.08e-0764
musculature of body5.08e-0764
skeletal muscle tissue5.22e-0762
striated muscle tissue5.22e-0762
myotome5.22e-0762
segmental subdivision of hindbrain5.82e-0712
hindbrain5.82e-0712
presumptive hindbrain5.82e-0712
trunk mesenchyme7.00e-07122
cardiovascular system8.02e-07109
organ system subdivision9.03e-07223


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)
MA0003.11.54338
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
MA0043.14.74607
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.15.73629
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
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.210.4956
MA0099.20.902716
MA0079.20.481578
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#187635.017155731697390.00791769806886330.0322749490111242
PAX5#507936.669565531177830.003370290999677260.0173104072841199
SP1#666735.69838137814090.005403962701712170.0246887340596727
USF1#739136.361499277207960.00388404057290560.0190578018977537



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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