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Coexpression cluster:C4530: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.63186,1.91835,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,2.64886,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,2.58159,0.960908,0.498519,1.39759,0.169933,2.26789,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.553386,0.794219,2.50498,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,2.15653,0.0768232
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.63186,1.91835,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,2.64886,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,2.58159,0.960908,0.498519,1.39759,0.169933,2.26789,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.553386,0.794219,2.50498,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,2.15653,0.0768232
|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;1.64148,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;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;2.4146,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;2.13518,MA0061.1;1.15625,MA0063.1;0,MA0066.1;0.941452,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;0.668628,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;4.76891,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;0.846801,MA0106.1;0.986396,MA0107.1;1.36919,MA0108.2;2.59836,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;1.35563,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;2.7939,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;3.41958,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;1.98824,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.757898,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;2.23118,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;0.455568,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;12.3219,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 22:07, 22 January 2013


Full id: C4530_duodenum_temporal_Mesenchymal_breast_Neurons_Fibroblast_Lens



Phase1 CAGE Peaks

Hg19::chr5:92918768..92918783,+p8@NR2F1
Hg19::chr5:92918789..92918800,+p12@NR2F1
Hg19::chr5:92918860..92918871,+p10@NR2F1


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
central nervous system6.09e-2781
cell layer1.72e-25309
neural plate1.85e-2582
presumptive neural plate1.85e-2582
neurectoderm2.93e-2586
anatomical cluster3.25e-25373
neural tube8.01e-2556
neural rod8.01e-2556
future spinal cord8.01e-2556
neural keel8.01e-2556
nervous system1.76e-2489
brain3.75e-2468
future brain3.75e-2468
epithelium6.41e-24306
regional part of nervous system4.48e-2353
regional part of brain4.48e-2353
tube1.57e-21192
anatomical conduit6.35e-21240
structure with developmental contribution from neural crest2.63e-20132
pre-chordal neural plate3.31e-1961
ecto-epithelium7.55e-19104
ectoderm-derived structure6.63e-17171
ectoderm6.63e-17171
presumptive ectoderm6.63e-17171
brain grey matter9.80e-1734
gray matter9.80e-1734
telencephalon1.67e-1634
regional part of forebrain2.29e-1641
forebrain2.29e-1641
anterior neural tube2.29e-1641
future forebrain2.29e-1641
regional part of telencephalon9.76e-1632
cerebral hemisphere1.00e-1532
multi-tissue structure1.06e-15342
organ system subdivision2.87e-15223
cerebral cortex9.30e-1425
pallium9.30e-1425
organ part5.36e-13218
regional part of cerebral cortex1.31e-1222
neocortex2.61e-1120
multi-cellular organism4.16e-11656
embryo8.49e-11592
posterior neural tube6.85e-1015
chordal neural plate6.85e-1015
developing anatomical structure1.19e-09581
germ layer1.67e-09560
germ layer / neural crest1.67e-09560
embryonic tissue1.67e-09560
presumptive structure1.67e-09560
germ layer / neural crest derived structure1.67e-09560
epiblast (generic)1.67e-09560
embryonic structure2.76e-09564
anatomical system4.69e-09624
anatomical group6.51e-09625
segmental subdivision of hindbrain3.36e-0812
hindbrain3.36e-0812
presumptive hindbrain3.36e-0812
organ5.88e-08503
simple squamous epithelium6.20e-0822
vasculature of organ1.44e-0711
pigment epithelium of eye2.64e-0711
squamous epithelium3.51e-0725
segmental subdivision of nervous system3.63e-0713
organ segment8.74e-0798
regional part of metencephalon9.01e-079
metencephalon9.01e-079
future metencephalon9.01e-079


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.11.64148
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
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
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
MA0105.10.846801
MA0106.10.986396
MA0107.11.36919
MA0108.22.59836
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.12.7939
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
MA0140.13.41958
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.22.23118
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
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.212.3219
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
EP300#203336.77394172622320.003216880500103790.0168210976092895
FOXA1#3169311.08141974938550.000734755275698670.00583463399016829
FOXA2#3170324.63046375266526.68983856509345e-050.00107605120883997
GATA1#2623313.56030814380040.0004009615963782630.00389218590613899
GATA2#2624312.7449317335540.0004829527704283790.0043867719943268
GTF2F1#2962312.73966087675770.0004835525047438590.00435660283324223
HDAC2#3066313.41562023662630.0004140761399857210.00393035517440414
HNF4A#3172323.13229036295378.07584663437677e-050.00123326999071162
HNF4G#3174328.75342252644684.20470658818262e-050.000759881210180316
JUND#372736.994663941871030.002921845042734990.0157482878886412
NANOG#79923329.24477848101273.99627955670032e-050.000740407026117128
PRDM1#6393131.8309557774614.35536935195671e-072.08464903642991e-05
RAD21#5885310.35503389545630.0009004912073565420.00667753487681836
REST#597839.650028716128020.001112636247114590.00770625485857157
RFX5#5993312.04791082719510.0005717246050312580.00486359420256248
RXRA#6256320.07461713913330.0001235730348432220.00165863567484787
SIN3A#2594235.408884726815140.006318961977991520.0278000787741462
SP1#666735.69838137814090.005403962701712170.0247667395385342
SRF#6722313.79717826216780.0003806615025800190.00376120214455578
TAL1#6886329.86861667744023.75103522793067e-050.00072199478099862
TCF7L2#6934310.77017656313730.0008003181298398380.00616859226290353
TRIM28#10155318.59052504526250.0001555969297255280.00197789529498593
ZNF263#1012738.221841637010680.001799043925565870.0109967428621195
ZZZ3#260093239.4132124352337.25894005043406e-084.38471046805831e-06



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:C4530&oldid=2573041"