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Coexpression cluster:C3386: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3386_gastric_Trabecular_Keratocytes_Neural_rhabdomyosarcoma_embryonic_Fibroblast
|id=C3386
}}

Latest revision as of 12:25, 17 September 2013


Full id: C3386_gastric_Trabecular_Keratocytes_Neural_rhabdomyosarcoma_embryonic_Fibroblast



Phase1 CAGE Peaks

Hg19::chr13:80915235..80915251,-p3@SPRY2
Hg19::chr13:80915252..80915274,-p1@SPRY2
Hg19::chr13:80915289..80915300,-p4@SPRY2


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>

Uber Anatomy
Ontology termp-valuen
cell layer3.04e-24309
epithelium6.07e-24306
anatomical cluster8.71e-23373
structure with developmental contribution from neural crest3.29e-21132
tube1.14e-20192
anatomical conduit1.16e-20240
multi-tissue structure1.14e-19342
multi-cellular organism3.28e-19656
anatomical system9.69e-19624
anatomical group2.24e-18625
embryo1.18e-16592
neural plate1.48e-1582
presumptive neural plate1.48e-1582
ecto-epithelium5.88e-15104
ectoderm-derived structure9.42e-15171
ectoderm9.42e-15171
presumptive ectoderm9.42e-15171
vasculature4.19e-1478
vascular system4.19e-1478
developing anatomical structure3.04e-13581
neurectoderm6.80e-1386
vessel1.63e-1268
epithelial vesicle3.46e-1278
epithelial tube3.68e-12117
artery4.21e-1242
arterial blood vessel4.21e-1242
arterial system4.21e-1242
dense mesenchyme tissue4.74e-1273
embryonic structure6.06e-12564
epithelial tube open at both ends6.21e-1259
blood vessel6.21e-1259
blood vasculature6.21e-1259
vascular cord6.21e-1259
neural tube1.09e-1156
neural rod1.09e-1156
future spinal cord1.09e-1156
neural keel1.09e-1156
paraxial mesoderm1.20e-1172
presumptive paraxial mesoderm1.20e-1172
central nervous system1.32e-1181
somite2.04e-1171
presomitic mesoderm2.04e-1171
presumptive segmental plate2.04e-1171
dermomyotome2.04e-1171
trunk paraxial mesoderm2.04e-1171
germ layer2.15e-11560
germ layer / neural crest2.15e-11560
embryonic tissue2.15e-11560
presumptive structure2.15e-11560
germ layer / neural crest derived structure2.15e-11560
epiblast (generic)2.15e-11560
nervous system5.40e-1189
splanchnic layer of lateral plate mesoderm6.11e-1183
regional part of nervous system1.31e-1053
regional part of brain1.31e-1053
systemic artery5.01e-1033
systemic arterial system5.01e-1033
organism subdivision9.39e-10264
pre-chordal neural plate1.69e-0961
mesenchyme4.30e-09160
entire embryonic mesenchyme4.30e-09160
multilaminar epithelium4.74e-0983
brain8.73e-0968
future brain8.73e-0968
skeletal muscle tissue1.21e-0862
striated muscle tissue1.21e-0862
myotome1.21e-0862
muscle tissue2.05e-0864
musculature2.05e-0864
musculature of body2.05e-0864
cardiovascular system3.05e-08109
circulatory system3.06e-08112
trunk mesenchyme3.83e-08122
brain grey matter8.30e-0834
gray matter8.30e-0834
organ1.15e-07503
unilaminar epithelium2.40e-07148
telencephalon2.53e-0734
regional part of forebrain4.30e-0741
forebrain4.30e-0741
anterior neural tube4.30e-0741
future forebrain4.30e-0741
regional part of telencephalon5.12e-0732
cerebral hemisphere6.30e-0732
organ part9.72e-07218


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
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0060.12.13518
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
MA0073.11.79391
MA0074.10.935474
MA0076.12.91768
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
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
MA0145.12.11725
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.23.88672
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.88736
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
MA0162.14.34338
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.26.90173
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
CCNT2#90536.336201576962630.003930750035764890.0189548251447617
CTBP2#1488362.71700033932814.049570681927e-060.000129218793904605
CTCF#1066435.360256373075030.0064925092527670.0278789233553874
E2F1#186934.907389214879320.008460985347239390.032424204626292
E2F6#187635.017155731697390.00791769806886330.0321157553446487
EBF1#187938.9064668465690.00141523283560980.00913450974094632
EGR1#195834.988179094810140.008056488137383440.0319660954555197
ELF1#199734.258097958807540.01295179875054610.0460892333540592
ELK4#2005316.2356816584680.0002336043955745990.00255336572155055
EP300#203336.77394172622320.003216880500103790.0167139835107875
FOS#235338.99795530889440.001372499272417130.00895834332304059
FOXA1#3169311.08141974938550.000734755275698670.00580198897918443
FOXA2#3170324.63046375266526.68983856509345e-050.00107126655918399
GABPB1#255337.067683836182170.002832212825417420.0153810761413224
GATA2#2624312.7449317335540.0004829527704283790.00436399934164817
GTF2B#2959331.94382993432423.06634405746243e-050.000626581700288239
HMGN3#932438.178547723350590.001827766942164210.0108484969125192
MAX#414936.452555509007120.003721913834265510.0186102819426847
MYC#460935.22228187160940.007020843755740150.0293722921409127
NANOG#79923329.24477848101273.99627955670032e-050.00073596797852623
NFYB#4801316.75979325353650.0002123649923296180.00245155161201647
PAX5#507936.669565531177830.003370290999677260.0172569408106728
RAD21#5885310.35503389545630.0009004912073565420.00662718632972376
REST#597839.650028716128020.001112636247114590.00766154262625441
RFX5#5993312.04791082719510.0005717246050312580.00483602057381223
TAF7#6879311.43306940492390.0006690181981945830.00541514311410091
TFAP2A#7020316.5186343730450.0002218033880766340.00247700214364153
TFAP2C#7022310.80922860986020.0007916746575753130.00614049086984836
TRIM28#10155318.59052504526250.0001555969297255280.00196664501314346
USF1#739136.361499277207960.00388404057290560.0189828870510407
YY1#752834.911170749853860.008441455341808260.0328495847098559
ZBTB7A#5134137.35190930787590.002516255860282270.0139814452964471
ZNF263#1012738.221841637010680.001799043925565870.0109111700663284



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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