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Coexpression cluster:C4353: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4353_heart_penis_aorta_smooth_sacrococcigeal_Mast_mesodermal
|id=C4353
}}

Latest revision as of 12:44, 17 September 2013


Full id: C4353_heart_penis_aorta_smooth_sacrococcigeal_Mast_mesodermal



Phase1 CAGE Peaks

Hg19::chr3:99594980..99594993,-p3@FILIP1L
Hg19::chr3:99594998..99595024,-p1@FILIP1L
Hg19::chr3:99595037..99595051,-p2@FILIP1L


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 cell6.54e-10121
muscle precursor cell9.14e-0858
myoblast9.14e-0858
multi-potent skeletal muscle stem cell9.14e-0858
muscle cell1.53e-0755
fibroblast2.56e-0776
contractile cell5.94e-0759
Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.61e-17656
anatomical system1.63e-15624
anatomical group2.20e-15625
trunk mesenchyme2.58e-13122
mesenchyme1.45e-12160
entire embryonic mesenchyme1.45e-12160
organism subdivision5.78e-12264
unilaminar epithelium2.83e-11148
epithelium7.51e-11306
cell layer1.04e-10309
anatomical cluster2.28e-10373
epithelial tube3.04e-10117
embryonic structure3.12e-10564
multilaminar epithelium3.55e-1083
multi-tissue structure4.13e-10342
muscle tissue4.87e-1064
musculature4.87e-1064
musculature of body4.87e-1064
developing anatomical structure7.83e-10581
trunk9.80e-10199
epithelial vesicle1.77e-0978
anatomical conduit3.09e-09240
skeletal muscle tissue3.41e-0962
striated muscle tissue3.41e-0962
myotome3.41e-0962
somite3.75e-0971
presomitic mesoderm3.75e-0971
presumptive segmental plate3.75e-0971
dermomyotome3.75e-0971
trunk paraxial mesoderm3.75e-0971
germ layer4.04e-09560
germ layer / neural crest4.04e-09560
embryonic tissue4.04e-09560
presumptive structure4.04e-09560
germ layer / neural crest derived structure4.04e-09560
epiblast (generic)4.04e-09560
paraxial mesoderm4.22e-0972
presumptive paraxial mesoderm4.22e-0972
dense mesenchyme tissue4.58e-0973
embryo2.11e-08592
splanchnic layer of lateral plate mesoderm2.14e-0883
mesoderm5.41e-08315
mesoderm-derived structure5.41e-08315
presumptive mesoderm5.41e-08315
organ6.57e-08503
vasculature7.83e-0878
vascular system7.83e-0878
vessel7.22e-0768


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
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.13.22835
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
MA0043.12.94978
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
MA0073.12.78116
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.14.76891
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
MA0114.10.549955
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
MA0145.10.752137
MA0146.13.73313
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
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
MA0162.13.52399
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
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#90536.336201576962630.003930750035764890.0190692866492591
CEBPB#105137.971147625824820.001974187055288560.0115559983111356
CTCF#1066435.360256373075030.0064925092527670.0280600527146589
E2F1#186934.907389214879320.008460985347239390.0326784086638931
E2F6#187635.017155731697390.00791769806886330.0323583043871655
EGR1#195834.988179094810140.008056488137383440.0321775809621855
ELF1#199734.258097958807540.01295179875054610.0464006898225948
FOXA1#3169311.08141974938550.000734755275698670.00582975812798703
JUN#3725312.51282919233630.0005103313992726250.00445490647012986
JUND#372736.994663941871030.002921845042734990.015727995795186
NFKB1#479035.488063424193840.006049381815655430.0270377621194521
POU5F1#54603335.4392014519062.63510205045339e-081.82256571554505e-06
RAD21#5885310.35503389545630.0009004912073565420.00666664784894803
SRF#6722313.79717826216780.0003806615025800190.00375871293069439
ZBTB7A#5134137.35190930787590.002516255860282270.0140645033873171
ZEB1#6935316.88843201754390.0002075486917327580.00243333832688342



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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