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Coexpression cluster:C4234: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,2.25583,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,1.26332,0.845342,0.635379,0.743951,1.00973,1.85641,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,2.33699,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,2.16826,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,2.69227,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,2.38768,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,1.63757,0.830777,3.47611,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,2.14918,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;3.20493,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,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;2.92613,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;6.95961,MA0059.1;6.94978,MA0060.1;0.492218,MA0061.1;0.456531,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;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,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;1.31954,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;3.82193,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;1.35563,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;2.18164,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;2.26598,MA0145.1;0.273764,MA0146.1;0.707589,MA0147.1;2.37462,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;1.60005,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;5.05652,MA0154.1;6.26194,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;1.55139,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
}}
}}

Revision as of 21:55, 22 January 2013


Full id: C4234_occipital_colon_parietal_duodenum_brain_temporal_spinal



Phase1 CAGE Peaks

Hg19::chr2:47572119..47572151,-p1@ENST00000413185
p1@ENST00000448713
p1@ENST00000450550
Hg19::chr2:47572187..47572202,-p2@ENST00000441997
Hg19::chr2:47572207..47572229,-p1@ENST00000441997


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
neural cell1.32e-0725
Uber Anatomy
Ontology termp-valuen
nervous system2.08e-4289
central nervous system2.38e-4281
neural tube9.29e-3956
neural rod9.29e-3956
future spinal cord9.29e-3956
neural keel9.29e-3956
organ system subdivision2.72e-36223
brain3.38e-3668
future brain3.38e-3668
regional part of nervous system6.22e-3653
regional part of brain6.22e-3653
adult organism8.10e-35114
anatomical cluster1.93e-34373
neural plate1.50e-3282
presumptive neural plate1.50e-3282
neurectoderm1.06e-2986
regional part of forebrain6.74e-2841
forebrain6.74e-2841
anterior neural tube6.74e-2841
future forebrain6.74e-2841
pre-chordal neural plate9.57e-2461
ecto-epithelium2.07e-23104
brain grey matter4.72e-2334
gray matter4.72e-2334
telencephalon1.07e-2234
regional part of telencephalon2.33e-2132
cerebral hemisphere5.75e-2132
anatomical conduit6.03e-21240
tube1.51e-20192
ectoderm-derived structure1.40e-19171
ectoderm1.40e-19171
presumptive ectoderm1.40e-19171
multi-tissue structure6.78e-19342
structure with developmental contribution from neural crest3.24e-17132
cerebral cortex9.99e-1725
pallium9.99e-1725
regional part of cerebral cortex7.32e-1622
epithelium8.36e-16306
organ part1.73e-15218
cell layer3.18e-15309
neocortex9.96e-1520
multi-cellular organism1.15e-14656
anatomical system4.84e-13624
organ5.74e-13503
anatomical group6.66e-13625
embryo4.63e-12592
posterior neural tube8.36e-1215
chordal neural plate8.36e-1215
gastrointestinal system2.48e-1025
segmental subdivision of nervous system5.32e-1013
developing anatomical structure1.05e-09581
intestine2.44e-0917
segmental subdivision of hindbrain3.85e-0912
hindbrain3.85e-0912
presumptive hindbrain3.85e-0912
trunk region element5.53e-09101
cavitated compound organ5.53e-0931
neural nucleus8.36e-089
nucleus of brain8.36e-089
basal ganglion2.69e-079
nuclear complex of neuraxis2.69e-079
aggregate regional part of brain2.69e-079
collection of basal ganglia2.69e-079
cerebral subcortex2.69e-079
organ segment7.15e-0798
embryonic structure8.47e-07564
regional part of metencephalon8.62e-079
metencephalon8.62e-079
future metencephalon8.62e-079
germ layer8.69e-07560
germ layer / neural crest8.69e-07560
embryonic tissue8.69e-07560
presumptive structure8.69e-07560
germ layer / neural crest derived structure8.69e-07560
epiblast (generic)8.69e-07560


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
MA0004.13.20493
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0046.12.92613
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.16.95961
MA0059.16.94978
MA0060.10.492218
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
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.13.82193
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
MA0116.10.560723
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
MA0136.12.18164
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.12.26598
MA0145.10.273764
MA0146.10.707589
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.15.05652
MA0154.16.26194
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
MA0080.21.55139
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
ATF3#467322.46317452600878.81932387510763e-050.00129821193261785
BHLHE40#8553344.87181354697741.10603738662898e-050.000285147960064537
CEBPB#105137.971147625824820.001974187055288560.0115514662931975
CTCF#1066435.360256373075030.0064925092527670.0280252603368354
EBF1#187938.9064668465690.00141523283560980.0091724898919109
ELF1#199734.258097958807540.01295179875054610.0463593429881515
EP300#203336.77394172622320.003216880500103790.0167857997776837
FOSL2#2355316.93020060456170.0002060162053171620.00243560408276195
FOXA1#3169311.08141974938550.000734755275698670.00582489040828096
FOXA2#3170324.63046375266526.68983856509345e-050.00107390109114632
HDAC2#3066313.41562023662630.0004140761399857210.00392286810449644
HNF4A#3172323.13229036295378.07584663437677e-050.00123075054231384
HNF4G#3174328.75342252644684.20470658818262e-050.000758306598796762
MAFK#7975327.10073313782995.02195559325033e-050.00085840919836902
MAX#414936.452555509007120.003721913834265510.0187016097636207
MYC#460935.22228187160940.007020843755740150.0295260490056272
REST#597839.650028716128020.001112636247114590.00769400893944254
RFX5#5993312.04791082719510.0005717246050312580.00485607888946483
RXRA#6256320.07461713913330.0001235730348432220.00165523203616664
SIN3A#2594235.408884726815140.006318961977991520.0277544818748194
SP1#666735.69838137814090.005403962701712170.0247135990105582
TCF7L2#6934310.77017656313730.0008003181298398380.00615451182993468
TRIM28#10155318.59052504526250.0001555969297255280.00197477065786904
USF1#739136.361499277207960.00388404057290560.0190802122950935
USF2#7392312.99219738506960.0004558979393427810.00422367824776197
YY1#752834.911170749853860.008441455341808260.0330193690802664



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:C4234&oldid=2572745"