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Coexpression cluster:C4013: Difference between revisions

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{{Coexpression_clusters
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9,0.177664,0.00039571,0.00384051,0.131761,0.160658,0.206239,0.0213159,0.28689,9.52066e-06,0.00756988,0.00698179,0.218052,0.0271615,0.11528,0.194982,7.10122e-05,0.281727,0.283218,0.249955,0.164638,0.00225856,0.0935776,5.90815e-05,7.38835e-06,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,4.78416e-08,0.00259055,0.00414049,0.101021,0.222548,6.17897e-08,0.157274,0.215705,0.00332029,0.205954,0.0107847|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,1.40888,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,1.54087,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,2.20639,0.498519,1.39759,0.169933,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,1.82176,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,1.76124,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,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;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;1.67416,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.04561,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;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;2.96495,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,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;0.752137,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,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;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.0373086,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4013_serous_Mammary_lung_colon_Prostate_small_Small
|id=C4013
}}

Latest revision as of 12:37, 17 September 2013


Full id: C4013_serous_Mammary_lung_colon_Prostate_small_Small



Phase1 CAGE Peaks

Hg19::chr20:14318211..14318232,-p1@FLRT3
Hg19::chr20:14318248..14318264,-p2@FLRT3
Hg19::chr20:14318270..14318289,-p3@FLRT3


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
endo-epithelial cell4.81e-1242
endodermal cell1.74e-1158
epithelial cell5.11e-10253
Uber Anatomy
Ontology termp-valuen
organ system subdivision3.17e-34223
multi-tissue structure1.09e-28342
anatomical cluster7.62e-26373
endoderm-derived structure1.19e-23160
endoderm1.19e-23160
presumptive endoderm1.19e-23160
ectoderm-derived structure6.09e-23171
ectoderm6.09e-23171
presumptive ectoderm6.09e-23171
multi-cellular organism5.91e-22656
organ1.50e-20503
digestive system2.30e-20145
digestive tract2.30e-20145
primitive gut2.30e-20145
embryo4.88e-20592
anatomical system3.34e-18624
anatomical group6.60e-18625
developing anatomical structure1.01e-17581
organ part3.08e-17218
embryonic structure2.88e-16564
ecto-epithelium4.35e-16104
central nervous system9.44e-1681
germ layer4.42e-15560
germ layer / neural crest4.42e-15560
embryonic tissue4.42e-15560
presumptive structure4.42e-15560
germ layer / neural crest derived structure4.42e-15560
epiblast (generic)4.42e-15560
epithelium5.17e-15306
cell layer5.66e-15309
subdivision of digestive tract1.06e-14118
nervous system1.47e-1489
brain4.49e-1468
future brain4.49e-1468
neural tube4.86e-1356
neural rod4.86e-1356
future spinal cord4.86e-1356
neural keel4.86e-1356
neural plate6.16e-1382
presumptive neural plate6.16e-1382
regional part of nervous system1.46e-1253
regional part of brain1.46e-1253
organism subdivision2.18e-12264
cerebral hemisphere2.55e-1232
endo-epithelium2.67e-1282
telencephalon4.47e-1234
neurectoderm6.06e-1286
brain grey matter6.81e-1234
gray matter6.81e-1234
cerebral cortex7.89e-1225
pallium7.89e-1225
pre-chordal neural plate8.43e-1261
regional part of telencephalon1.00e-1132
regional part of forebrain1.51e-1141
forebrain1.51e-1141
anterior neural tube1.51e-1141
future forebrain1.51e-1141
regional part of cerebral cortex2.05e-1122
structure with developmental contribution from neural crest4.70e-11132
neocortex1.12e-1020
respiratory system2.42e-0974
anatomical conduit3.93e-09240
gut epithelium5.55e-0954
orifice1.73e-0836
adult organism2.66e-08114
gland3.61e-0859
anterior region of body1.60e-0762
craniocervical region1.60e-0762
head1.72e-0756
surface structure3.06e-0799
hindgut4.35e-0719
foregut7.54e-0787
epithelial bud8.13e-0737
organ segment9.09e-0798


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.12.96495
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
MA0146.10.107247
MA0147.10.565108
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
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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#105137.971147625824820.001974187055288560.0115333737129989
CTCF#1066435.360256373075030.0064925092527670.0279824683827061
FOSL2#2355316.93020060456170.0002060162053171620.00243230007541477
GATA3#2625327.2365163572064.94721007899563e-050.000852047614512244
GTF2F1#2962312.73966087675770.0004835525047438590.00434573100791188
JUN#3725312.51282919233630.0005103313992726250.0044471006265026
JUND#372736.994663941871030.002921845042734990.0156964443402191
NFKB1#479035.488063424193840.006049381815655430.0269880985666483
RAD21#5885310.35503389545630.0009004912073565420.00664826814683372
RFX5#5993312.04791082719510.0005717246050312580.00485134433091157
SMC3#9126315.04493284493280.0002935825420371870.00309430488523784
TRIM28#10155318.59052504526250.0001555969297255280.00197237380065595
YY1#752834.911170749853860.008441455341808260.0329810764446939
ZNF143#7702313.50087655222790.0004062804962997170.00389566000303398
ZNF263#1012738.221841637010680.001799043925565870.0109557054543542



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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