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Coexpression cluster:C4736: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4736_Mesenchymal_Alveolar_Renal_Whole_blood_Pericytes_heart
|id=C4736
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4736_Mesenchymal_Alveolar_Renal_Whole_blood_Pericytes_heart



Phase1 CAGE Peaks

Hg19::chr8:145158581..145158693,-p1@SHARPIN
Hg19::chr8:145159376..145159407,+p1@MAF1
Hg19::chr8:145159415..145159438,+p2@MAF1


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 cell2.44e-10121
lining cell1.46e-0958
barrier cell1.46e-0958
meso-epithelial cell1.53e-0945
endothelial cell1.69e-0836
epithelial cell1.21e-07253
Uber Anatomy
Ontology termp-valuen
circulatory system4.43e-12112
cardiovascular system7.93e-11109
epithelial tube4.15e-09117
splanchnic layer of lateral plate mesoderm5.53e-0983
vessel4.06e-0868
vasculature5.87e-0878
vascular system5.87e-0878
epithelial tube open at both ends6.96e-0859
blood vessel6.96e-0859
blood vasculature6.96e-0859
vascular cord6.96e-0859
trunk8.84e-07199


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
MA0057.10.886807
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
MA0073.10.990225
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.14.65896
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
MA0139.13.97071
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.12.83144
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
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#90536.336201576962630.003930750035764890.0191261462441879
EGR1#195834.988179094810140.008056488137383440.0322627133658048
ELF1#199734.258097958807540.01295179875054610.0465139750939886
GABPB1#255337.067683836182170.002832212825417420.0154873802436656
HNF4A#3172323.13229036295378.07584663437677e-050.00123453358701358
HNF4G#3174328.75342252644684.20470658818262e-050.00076053922993281
IRF1#365937.63716375356390.002244692747297240.012877421907991
IRF3#3661231.32130147432640.001339514673320110.00888013031400784
MYC#460935.22228187160940.007020843755740150.0296214713179989
NANOG#79923329.24477848101273.99627955670032e-050.000741459301158687
NFYA#4800212.28372046655370.008516011403724430.0325003184606291
NFYB#4801211.17319550235760.01025467135054530.0381636895976766
PAX5#507936.669565531177830.003370290999677260.0173727763543405
PBX3#5090214.60967512449610.006056122473217890.0268586935742666
SIN3A#2594235.408884726815140.006318961977991520.0278387779473322
SP1#666735.69838137814090.005403962701712170.0247972082866484
SP2#6668326.15353049384465.58768218891694e-050.000942917983726443
SREBF1#6720231.33723296032550.00133816265136180.00887905776020174
STAT1#6772213.80439166479950.006770931708444080.0287634466828632
THAP1#55145220.91276306856750.002983447413736940.0158787272304577
ZBTB33#10009221.10981668665410.002928597060603240.0156425995198866
ZBTB7A#5134137.35190930787590.002516255860282270.0140999702646217
ZNF143#7702313.50087655222790.0004062804962997170.00390534088845339



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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