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Coexpression cluster:C2973: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,1.18351,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,1.86765,1.21459,0.534793,1.11965,0.599922,0.137917,2.47502,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,1.72524,0.939121,0.808003,0.69206,1.55608,1.02504,2.18821,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,0.414196,0.396746,2.54768,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.95969,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.946807,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,2.76728,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,1.54007,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224
|tfbs_overrepresentation_jaspar=MA0003.1;2.61626,MA0004.1;1.93041,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.758317,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;2.8588,MA0059.1;4.12962,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;2.1667,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;1.74184,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;6.72819,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;1.55117,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;1.70974,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.62945,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.481578,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0
}}
}}

Revision as of 21:03, 22 January 2013


Full id: C2973_Mesenchymal_Alveolar_Renal_Pericytes_Hepatic_Smooth_Astrocyte



Phase1 CAGE Peaks

Hg19::chr10:104192322..104192379,-p1@CUEDC2
Hg19::chr2:242447962..242447981,-p3@STK25
Hg19::chr2:242447983..242448034,-p1@STK25


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
embryonic cell2.52e-29250
mesodermal cell4.48e-24121
non-terminally differentiated cell1.80e-17106
contractile cell1.88e-1659
electrically responsive cell3.68e-1561
electrically active cell3.68e-1561
muscle cell3.83e-1455
muscle precursor cell4.58e-1458
myoblast4.58e-1458
multi-potent skeletal muscle stem cell4.58e-1458
meso-epithelial cell2.54e-1145
smooth muscle cell3.38e-1143
smooth muscle myoblast3.38e-1143
endothelial cell7.00e-1136
vascular associated smooth muscle cell1.41e-0932
lining cell7.95e-0958
barrier cell7.95e-0958
epithelial cell of nephron1.98e-0815
ectodermal cell3.30e-0872
endothelial cell of vascular tree3.30e-0824
blood vessel endothelial cell9.05e-0818
embryonic blood vessel endothelial progenitor cell9.05e-0818
kidney cortical cell2.77e-0712
renal cortical epithelial cell2.77e-0712
Uber Anatomy
Ontology termp-valuen
cell layer4.31e-30309
epithelium1.39e-29306
anatomical cluster3.69e-22373
epithelial vesicle2.38e-2178
multilaminar epithelium3.59e-1983
multi-tissue structure4.04e-19342
vasculature4.34e-1978
vascular system4.34e-1978
paraxial mesoderm4.08e-1872
presumptive paraxial mesoderm4.08e-1872
dense mesenchyme tissue5.25e-1873
somite8.15e-1871
presomitic mesoderm8.15e-1871
presumptive segmental plate8.15e-1871
dermomyotome8.15e-1871
trunk paraxial mesoderm8.15e-1871
mesenchyme3.96e-17160
entire embryonic mesenchyme3.96e-17160
tube8.04e-17192
epithelial tube8.77e-17117
unilaminar epithelium9.04e-17148
skeletal muscle tissue8.29e-1662
striated muscle tissue8.29e-1662
myotome8.29e-1662
anatomical conduit5.74e-15240
vessel9.78e-1568
organism subdivision1.10e-14264
muscle tissue1.31e-1464
musculature1.31e-1464
musculature of body1.31e-1464
trunk mesenchyme4.30e-14122
epithelial tube open at both ends7.55e-1459
blood vessel7.55e-1459
blood vasculature7.55e-1459
vascular cord7.55e-1459
splanchnic layer of lateral plate mesoderm1.04e-1383
trunk4.27e-12199
multi-cellular organism5.14e-12656
ectoderm-derived structure3.83e-11171
ectoderm3.83e-11171
presumptive ectoderm3.83e-11171
artery7.74e-1142
arterial blood vessel7.74e-1142
arterial system7.74e-1142
circulatory system1.46e-10112
cardiovascular system2.56e-10109
organ part6.85e-10218
anatomical system1.45e-09624
structure with developmental contribution from neural crest1.86e-09132
anatomical group2.61e-09625
developing anatomical structure1.75e-08581
nephron epithelium1.98e-0815
renal tubule1.98e-0815
nephron tubule1.98e-0815
nephron1.98e-0815
uriniferous tubule1.98e-0815
nephrogenic mesenchyme1.98e-0815
embryo2.21e-08592
excretory tube4.28e-0816
kidney epithelium4.28e-0816
parenchyma6.90e-0815
blood vessel endothelium9.05e-0818
endothelium9.05e-0818
cardiovascular system endothelium9.05e-0818
systemic artery1.42e-0733
systemic arterial system1.42e-0733
ecto-epithelium2.33e-07104
cortex of kidney2.77e-0712
renal parenchyma2.77e-0712
compound organ4.40e-0768
embryonic structure8.20e-07564
squamous epithelium9.28e-0725


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)
MA0003.12.61626
MA0004.11.93041
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
MA0028.11.58389
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
MA0058.12.8588
MA0059.14.12962
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.16.72819
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
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
MA0146.11.70974
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
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
MA0162.11.43223
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
ATF3#467214.97544968400580.005768294540793880.0259413044630742
BCLAF1#9774321.65264761012189.8473954032885e-050.0013879245998975
CCNT2#90536.336201576962630.003930750035764890.0189007183694866
CHD2#1106310.34402283411690.0009033701102746880.00658158848601173
E2F1#186934.907389214879320.008460985347239390.0323293033578581
E2F6#187635.017155731697390.00791769806886330.0320175192091228
EGR1#195834.988179094810140.008056488137383440.0318837273429401
ELF1#199734.258097958807540.01295179875054610.0459717546801347
ESR1#2099220.51240219743630.003099741577095180.0162999803922382
ETS1#211339.728760922202340.001085840092584840.00759368243132903
GABPB1#255337.067683836182170.002832212825417420.0153595116457457
IRF1#365937.63716375356390.002244692747297240.0127541192445991
MAX#414936.452555509007120.003721913834265510.0185622921033788
MYC#460935.22228187160940.007020843755740150.0293006953448849
NFKB1#479035.488063424193840.006049381815655430.026841336878462
PAX5#507936.669565531177830.003370290999677260.0172172677418946
SETDB1#9869226.8800174520070.001814468907964410.0108902544841615
SIX5#147912317.0867153554590.0002004060546325010.00238929314380865
SP1#666735.69838137814090.005403962701712170.0245299226618618
SRF#6722313.79717826216780.0003806615025800190.00373751120315452
TFAP2A#7020211.01242291536330.01054990655215560.0389873567956046
TFAP2C#7022310.80922860986020.0007916746575753130.00612638630427594
TRIM28#10155318.59052504526250.0001555969297255280.00196450528815333
USF1#739136.361499277207960.00388404057290560.0189394580910303
YY1#752834.911170749853860.008441455341808260.0327714353744373
ZBTB33#10009331.66472502998123.14815888737575e-050.000632776301075127
ZNF143#7702313.50087655222790.0004062804962997170.00387502545689919



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2973&oldid=2571484"