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Coexpression cluster:C3995: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3995_occipital_cerebral_spinal_small_temporal_heart_rectum
|id=C3995
|ontology_enrichment_celltype=CL:0000055!1.08e-09!180;CL:0000192!7.54e-09!42;CL:0000514!7.54e-09!42;CL:0000359!4.26e-08!32;CL:0000680!4.84e-08!57;CL:0000056!4.84e-08!57;CL:0000355!4.84e-08!57;CL:0000187!4.25e-07!54
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.89e-25!57;UBERON:0005068!2.89e-25!57;UBERON:0006241!2.89e-25!57;UBERON:0007135!2.89e-25!57;UBERON:0007023!2.48e-24!115;UBERON:0002616!4.53e-23!59;UBERON:0003080!2.99e-21!42;UBERON:0002780!3.80e-21!41;UBERON:0001890!3.80e-21!41;UBERON:0006240!3.80e-21!41;UBERON:0000955!2.81e-20!69;UBERON:0006238!2.81e-20!69;UBERON:0001017!1.07e-19!82;UBERON:0005743!1.71e-19!86;UBERON:0002346!3.02e-19!90;UBERON:0003075!3.57e-19!86;UBERON:0007284!3.57e-19!86;UBERON:0002020!2.88e-18!34;UBERON:0003528!2.88e-18!34;UBERON:0001869!1.36e-17!32;UBERON:0001893!1.47e-17!34;UBERON:0000073!1.72e-17!94;UBERON:0001016!1.72e-17!94;UBERON:0002791!4.41e-17!33;UBERON:0003056!4.05e-16!61;UBERON:0000475!9.64e-16!365;UBERON:0000025!2.09e-15!194;UBERON:0002619!6.09e-15!22;UBERON:0000483!1.91e-14!309;UBERON:0000477!2.07e-14!286;UBERON:0000956!5.79e-14!25;UBERON:0000203!5.79e-14!25;UBERON:0000119!5.96e-14!312;UBERON:0001950!1.15e-13!20;UBERON:0000468!5.55e-13!659;UBERON:0000153!4.66e-12!129;UBERON:0007811!4.66e-12!129;UBERON:0000033!5.08e-12!123;UBERON:0004111!5.83e-12!241;UBERON:0000481!1.02e-11!347;UBERON:0000924!2.04e-10!173;UBERON:0006601!2.04e-10!173;UBERON:0004121!3.72e-10!169;UBERON:0000467!5.06e-10!625;UBERON:0000914!5.12e-10!83;UBERON:0002329!5.12e-10!83;UBERON:0003077!5.12e-10!83;UBERON:0003059!5.12e-10!83;UBERON:0007282!5.12e-10!83;UBERON:0009618!5.12e-10!83;UBERON:0007285!5.12e-10!83;UBERON:0002050!7.18e-10!605;UBERON:0005423!7.18e-10!605;UBERON:0000480!8.27e-10!626;UBERON:0000922!8.84e-10!612;UBERON:0000923!1.31e-09!604;UBERON:0005291!1.31e-09!604;UBERON:0006598!1.31e-09!604;UBERON:0002532!1.31e-09!604;UBERON:0004290!2.20e-09!70;UBERON:0002385!8.71e-09!63;UBERON:0001015!8.71e-09!63;UBERON:0000383!8.71e-09!63;UBERON:0000479!9.51e-09!787;UBERON:0001134!1.67e-08!61;UBERON:0002036!1.67e-08!61;UBERON:0003082!1.67e-08!61;UBERON:0001981!1.15e-07!60;UBERON:0007500!1.15e-07!60;UBERON:0004537!1.15e-07!60;UBERON:0006965!1.15e-07!60;UBERON:0001637!1.66e-07!42;UBERON:0003509!1.66e-07!42;UBERON:0004572!1.66e-07!42;UBERON:0004573!6.04e-07!33;UBERON:0004571!6.04e-07!33
}}

Latest revision as of 12:37, 17 September 2013


Full id: C3995_occipital_cerebral_spinal_small_temporal_heart_rectum



Phase1 CAGE Peaks

Hg19::chr1:72748492..72748510,-p5@NEGR1
Hg19::chr1:72748523..72748538,-p3@NEGR1
Hg19::chr1:72748551..72748570,-p4@NEGR1


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
smooth muscle cell3.00e-0843
smooth muscle myoblast3.00e-0843
vascular associated smooth muscle cell7.96e-0832
muscle precursor cell1.21e-0758
myoblast1.21e-0758
multi-potent skeletal muscle stem cell1.21e-0758
muscle cell7.97e-0755
Uber Anatomy
Ontology termp-valuen
neural tube4.36e-2456
neural rod4.36e-2456
future spinal cord4.36e-2456
neural keel4.36e-2456
adult organism1.49e-23114
regional part of nervous system2.69e-2253
regional part of brain2.69e-2253
regional part of forebrain4.97e-2041
forebrain4.97e-2041
anterior neural tube4.97e-2041
future forebrain4.97e-2041
brain1.18e-1968
future brain1.18e-1968
central nervous system1.44e-1981
neurectoderm3.37e-1886
neural plate4.39e-1882
presumptive neural plate4.39e-1882
structure with developmental contribution from neural crest7.99e-18132
brain grey matter1.92e-1734
gray matter1.92e-1734
nervous system2.09e-1789
cerebral hemisphere6.19e-1732
telencephalon1.06e-1634
regional part of telencephalon2.68e-1632
ecto-epithelium1.21e-14104
tube2.06e-14192
pre-chordal neural plate2.70e-1461
regional part of cerebral cortex4.76e-1422
epithelium9.85e-14306
multi-tissue structure1.54e-13342
cerebral cortex2.58e-1325
pallium2.58e-1325
cell layer3.10e-13309
neocortex8.60e-1320
multi-cellular organism1.36e-12656
embryonic structure4.87e-11564
anatomical conduit4.88e-11240
anatomical cluster4.96e-11373
germ layer6.68e-11560
germ layer / neural crest6.68e-11560
embryonic tissue6.68e-11560
presumptive structure6.68e-11560
germ layer / neural crest derived structure6.68e-11560
epiblast (generic)6.68e-11560
ectoderm-derived structure1.97e-10171
ectoderm1.97e-10171
presumptive ectoderm1.97e-10171
developing anatomical structure5.49e-10581
embryo1.22e-09592
paraxial mesoderm1.27e-0972
presumptive paraxial mesoderm1.27e-0972
tissue1.40e-09773
anatomical system2.21e-09624
anatomical group3.51e-09625
somite3.58e-0971
presomitic mesoderm3.58e-0971
presumptive segmental plate3.58e-0971
dermomyotome3.58e-0971
trunk paraxial mesoderm3.58e-0971
dense mesenchyme tissue3.68e-0973
muscle tissue1.34e-0864
musculature1.34e-0864
musculature of body1.34e-0864
skeletal muscle tissue3.28e-0862
striated muscle tissue3.28e-0862
myotome3.28e-0862
organ system subdivision5.86e-08223
artery2.87e-0742
arterial blood vessel2.87e-0742
arterial system2.87e-0742
epithelial vesicle2.97e-0778
epithelial tube open at both ends4.23e-0759
blood vessel4.23e-0759
blood vasculature4.23e-0759
vascular cord4.23e-0759


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.13.71555
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
MA0055.119.8275
MA0056.10
MA0057.12.4146
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
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
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
MA0105.10.31555
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
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.16.40038
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.8725
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
CEBPB#105137.971147625824820.001974187055288560.0115314385831813
CTCF#1066435.360256373075030.0064925092527670.0279755414576175
E2F1#186934.907389214879320.008460985347239390.0325748091820081
ESR1#2099330.76860329615453.43136389821584e-050.000676804937045824
RAD21#5885310.35503389545630.0009004912073565420.00664638877774628



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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