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Coexpression cluster:C291: Difference between revisions

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{{Coexpression_clusters
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96e-05,0.000201616,0.390621,0.888399,0.217962,0.50103,0.0177663,0.721126,0.112564,0.0048173,0.940691,0.843151,0.155553,0.00412705,0.248147,0.0398861,0.683127,0.441575,0.00348339,6.66983e-05,0.00237383,0.000113551,0.16068,1.54719e-06,0.876823,0.00933751,0.0179271,0.78133,0.0539776,0.0103212,0.622102,0.00851536,0.783885,0.426105,0.0105571,0.253118,0.178633,0.122782,0.00225155,0.00440839,3.85077e-11,0.107404,0.817806,0.00285965,0.000789702,0.904297,0.126421,0.00459562,0.00356728,0.464225,0.0100538,0.845864,0.0205963,9.62897e-06,0.714386,0.00204082,0.477869,0.26825,0.225215,0.00204546,0.576661,0.706085,0.000476343,0.0076152,0.869207,0.125986,0.159588,0.695628,0.853081,0.0220548,0.395284,0.371674,0.639419,0.953073,0.0985146,0.827916,0.733018,0.377264,0.734667,0.877552,0.664183,0.402769,0.0619267,0.497641,0.422228,0.000919025,0.0730695,0.967007,0.0166626,0.330398,0.387656,0.497701,0.975281,0.575226,0.793333,0.0310759,0.110881,0.584122,0.574827,0.633092,0.38491,0.762288,0.307774,0.94545,0.890374,0.0553581,0.000425699,0.610353,0.447541,0.786063,0.310492,0.640258,0.2612,0.30503,0.82799,0.671359,0.336525,0.262843,0.334773,0.288274,0.437715,8.47779e-05,0.544464,0.495298,0.0445985,0.237807,0.605523,0.448241,0.847128,0.0197129,0.814341,0.593703,0.287409,0.464024,0.87915,0.103748,0.308514,0.281595,0.000163049,5.57487e-05,0.0458076,0.634007,0.0115044,0.695459,0.132272,0.182731,0.801798,0.301391,0.446211,0.1627,0.84647,0.0674969,0.258053,0.656015,0.608617,0.247145,0.0105856,0.71965,0.782161,0.5273,0.114812,0.182303,0.222943,0.220254,0.711798,0.153996,0.03396,0.312166,0.763867,0.777843,0.775845,0.642977,0.184491,0.860957,0.875248,5.14539e-05,0.842698,0.492814,0.554282,0.555443,0.692236,0.696185,0.456528,0.55518,0.338422,0.458462,0.459479,0.00422127,0.35214,0.371266,0.130078,0.780103,0.621796,0.56818,0.0745125,0.481663,0.634519,0.687548,0.000256266,0.0925191,0.484,0.270267,0.0511571,0.422522,0.627164,0.000725837,0.409087,0.231266,0.434011,0.0269414,0.293478,0.148562,0.0189992,0.000572898,0.994468,0.142798,0.00931127,0.866006,0.0171842,0.874096,0.726509,0.438931,0.112226,0.958171,0.106242,0.826847,0.83558,0.698583,0.17225,0.83411,0.61613,0.0952578,0.954328,0.363651,0.0114403,0.491165,0.718667,0.763309,0.0163652,0.723372,0.445206,0.771959,0.732258,0.201625,0.936873,0.250376,0.841713,0.66105,0.491987,0.790271,0.0135331,0.158302,0.24449,0.690748,0.0691529,0.656842,0.0713076|tfbs_overrepresentation_for_novel_motifs=0.0770214,1.22656,0.187803,0.189922,0.478337,0.0503874,0.270416,0.923492,0.295826,0.0649359,0.159384,0.0977176,0.182567,0.0739528,0.47421,0.324158,0.196131,0.178102,0.212955,0.377983,0.187882,2.63684,0.0478871,0.00922266,0.253509,0.108506,0.137217,0.178548,0.139457,1.57823,0.139887,0.21983,0.403472,0.874359,0.0339912,0.349034,0.0327521,0.421985,0.167985,0.390114,0.210352,0.126154,0.204517,1.0256,4.60715,0.0926201,0.0791092,0.0379637,0.764413,0.284883,0.369823,0.0840973,0.691609,0.749168,0.387839,0.0751381,0.0530358,0.224212,0.186595,0.0620937,0.247394,0.274444,0.46219,0.178993,0.295737,0.158602,0.459731,0.785997,0.213036,0.638058,0.516104,0.961964,0.00834401,0.38625,0.0927233,0.374972,0.646321,0.973563,0.210927,1.9485,0.986502,0.178342,0.0876498,0.182029,0.34606,0.014618,0.0288084,5.05838,0.128924,0.878893,0.538954,0.869111,0.230992,1.19262,1.04486,0.292557,0.338017,0.26018,0.131366,0.220767,0.00434495,0.644356,0.256288,1.71732,0.152013,0.0397459,0.188528,0.5397,0.0241148,0.0418043,0.39326,0.70755,0.0690617,0.0438478,0.497839,0.204416,0.122038,0.138852,1.48107,0.267437,0.379694,0.799202,0.185557,0.0926673,0.593672,0.169305,0.263084,0.234349,0.413768,0.160055,0.870277,0.035737,0.425444,1.05603,0.550109,0.715019,0.577272,1.09564,0.513551,1.31743,0.928445,0.481891,0.265072,0.257717,0.465337,0.470067,0.14366,1.1621,0.123437,0.876823,0.764451,0.000924276,0.326314,0.156546,0.0798956,0.665555,0.120517,0.676701,0.253599,0.406736,0.480867,0.312435,0.210417,0.21574,0.162274,1.52555,0.807117,0.961011,1.47266|tfbs_overrepresentation_jaspar=MA0003.1;1.08123,MA0004.1;0.164226,MA0006.1;0.00959877,MA0007.1;0.340746,MA0009.1;0.295212,MA0014.1;0.928098,MA0017.1;0.597798,MA0019.1;0.100079,MA0024.1;0.631021,MA0025.1;0.398381,MA0027.1;1.79461,MA0028.1;0.0116229,MA0029.1;0.234549,MA0030.1;1.2023,MA0031.1;1.039,MA0038.1;0.0798193,MA0040.1;0.238542,MA0041.1;0.408255,MA0042.1;1.40245,MA0043.1;0.295444,MA0046.1;0.28722,MA0048.1;0.176175,MA0050.1;0.0389209,MA0051.1;0.268697,MA0052.1;0.241195,MA0055.1;1.23332,MA0056.1;0,MA0057.1;1.08855,MA0058.1;0.217702,MA0059.1;1.38385,MA0060.1;0.0347326,MA0061.1;0.971848,MA0063.1;0,MA0066.1;0.0800001,MA0067.1;0.553259,MA0068.1;0.690544,MA0069.1;1.41712,MA0070.1;0.276295,MA0071.1;0.496436,MA0072.1;0.273057,MA0073.1;15.8781,MA0074.1;0.267816,MA0076.1;0.0224905,MA0077.1;0.267535,MA0078.1;0.394373,MA0081.1;0.679275,MA0083.1;0.300765,MA0084.1;0.721137,MA0087.1;0.271301,MA0088.1;3.27374,MA0089.1;0,MA0090.1;0.790582,MA0091.1;1.48244,MA0092.1;0.312424,MA0093.1;0.13733,MA0095.1;0,MA0098.1;0,MA0100.1;0.0858032,MA0101.1;0.75277,MA0103.1;1.32309,MA0105.1;0.298475,MA0106.1;1.62838,MA0107.1;0.0681419,MA0108.2;1.63126,MA0109.1;0,MA0111.1;2.13428,MA0113.1;0.702295,MA0114.1;0.272528,MA0115.1;0.487485,MA0116.1;0.293865,MA0117.1;0.32334,MA0119.1;0.074899,MA0122.1;0.343167,MA0124.1;0.452592,MA0125.1;0.384032,MA0130.1;0,MA0131.1;0.134702,MA0132.1;0,MA0133.1;0,MA0135.1;1.53776,MA0136.1;0.0828349,MA0139.1;0.0477972,MA0140.1;0.226615,MA0141.1;0.410305,MA0142.1;5.46563,MA0143.1;2.98705,MA0144.1;0.125436,MA0145.1;2.57894,MA0146.1;0.0107116,MA0147.1;0.164952,MA0148.1;0.188509,MA0149.1;0.817013,MA0062.2;0.00069578,MA0035.2;0.0630244,MA0039.2;0.805374,MA0138.2;0.125638,MA0002.2;0.262615,MA0137.2;0.160933,MA0104.2;0.458521,MA0047.2;0.0926231,MA0112.2;2.42092,MA0065.2;1.75176,MA0150.1;0.0242915,MA0151.1;0,MA0152.1;0.0657794,MA0153.1;0.370648,MA0154.1;0.190637,MA0155.1;1.02948,MA0156.1;0.0128364,MA0157.1;0.894256,MA0158.1;0,MA0159.1;0.304415,MA0160.1;0.204102,MA0161.1;0,MA0162.1;0.0231338,MA0163.1;0.595802,MA0164.1;0.112235,MA0080.2;0.0499414,MA0018.2;0.325809,MA0099.2;0.0659162,MA0079.2;3.93054,MA0102.2;0.755388,MA0258.1;2.4979,MA0259.1;0.0810548,MA0442.1;0}}
|full_id=C291_spinal_substantia_retina_medulla_tongue_skeletal_trachea
|id=C291
}}

Latest revision as of 11:15, 17 September 2013


Full id: C291_spinal_substantia_retina_medulla_tongue_skeletal_trachea



Phase1 CAGE Peaks

Hg19::chr10:104184955..104184965,-p4@CUEDC2
Hg19::chr10:60936793..60936819,-p@chr10:60936793..60936819
-
Hg19::chr11:125366211..125366212,-p14@FEZ1
Hg19::chr17:42984119..42984130,-p43@GFAP
Hg19::chr17:42984138..42984151,-p38@GFAP
Hg19::chr17:42984459..42984521,+p@chr17:42984459..42984521
+
Hg19::chr17:42984550..42984567,+p@chr17:42984550..42984567
+
Hg19::chr17:42984604..42984618,+p@chr17:42984604..42984618
+
Hg19::chr17:42989173..42989181,-p40@GFAP
Hg19::chr17:73504580..73504588,-p@chr17:73504580..73504588
-
Hg19::chr19:1452223..1452232,+p@chr19:1452223..1452232
+
Hg19::chr19:40919278..40919294,-p2@PRX
Hg19::chr1:156404868..156404881,+p@chr1:156404868..156404881
+
Hg19::chr1:156404895..156404923,+p@chr1:156404895..156404923
+
Hg19::chr1:156404975..156404990,+p@chr1:156404975..156404990
+
Hg19::chr1:161275051..161275059,-p@chr1:161275051..161275059
-
Hg19::chr1:161275062..161275086,-p@chr1:161275062..161275086
-
Hg19::chr1:161275096..161275109,-p@chr1:161275096..161275109
-
Hg19::chr1:161275111..161275127,-p@chr1:161275111..161275127
-
Hg19::chr1:161275189..161275203,-p@chr1:161275189..161275203
-
Hg19::chr1:161275238..161275250,-p@chr1:161275238..161275250
-
Hg19::chr1:161275265..161275277,-p@chr1:161275265..161275277
-
Hg19::chr1:161275395..161275412,-p@chr1:161275395..161275412
-
Hg19::chr1:161275623..161275644,-p@chr1:161275623..161275644
-
Hg19::chr1:161276191..161276202,-p6@MPZ
Hg19::chr1:161276686..161276694,-p11@MPZ
Hg19::chr1:161279749..161279764,-p1@MPZ
Hg19::chr1:44991346..44991355,+p@chr1:44991346..44991355
+
Hg19::chr20:52573198..52573199,-p@chr20:52573198..52573199
-
Hg19::chr2:128403624..128403631,+p4@GPR17
Hg19::chr2:128403720..128403732,+p1@GPR17
Hg19::chr2:241521605..241521654,-p@chr2:241521605..241521654
-
Hg19::chr3:44062980..44062993,+p@chr3:44062980..44062993
+
Hg19::chr4:115519490..115519496,+p11@UGT8
Hg19::chr5:123774243..123774262,-p@chr5:123774243..123774262
-
Hg19::chr5:123774265..123774292,-p@chr5:123774265..123774292
-
Hg19::chr5:123774307..123774326,-p@chr5:123774307..123774326
-
Hg19::chr5:146435694..146435705,-p23@PPP2R2B
Hg19::chr6:133424178..133424190,-p@chr6:133424178..133424190
-
Hg19::chr7:29966288..29966313,-p@chr7:29966288..29966313
-
Hg19::chr7:33842781..33842787,-p1@ENST00000440034
Hg19::chr7:4998664..4998674,-p2@MMD2
Hg19::chr7:99531868..99531881,-p@chr7:99531868..99531881
-
Hg19::chr9:90113407..90113437,+p11@DAPK1


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

GO IDGO nameFDR corrected p-value
GO:0007638mechanosensory behavior0.000225625857182879
GO:0032502developmental process0.000680714741513836
GO:0009612response to mechanical stimulus0.000680714741513836
GO:0007422peripheral nervous system development0.00103494969512009
GO:0007399nervous system development0.00143356170058839
GO:0008489UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity0.00754747717880883
GO:00038512-hydroxyacylsphingosine 1-beta-galactosyltransferase activity0.00754747717880883
GO:0048468cell development0.00754747717880883
GO:0048731system development0.0170389325473447
GO:0045217intercellular junction maintenance0.0170389325473447
GO:0009628response to abiotic stimulus0.0180450614628599
GO:0048869cellular developmental process0.0193185416021582
GO:0030154cell differentiation0.0193185416021582
GO:0048856anatomical structure development0.0239334495934795
GO:0008219cell death0.0239334495934795
GO:0016265death0.0239334495934795
GO:0043015gamma-tubulin binding0.0267100411830768
GO:0006688glycosphingolipid biosynthetic process0.0309604441808687
GO:0007275multicellular organismal development0.0309604441808687
GO:0007610behavior0.0309604441808687
GO:0019226transmission of nerve impulse0.0369535581590065
GO:0009247glycolipid biosynthetic process0.038663346172115
GO:0019835cytolysis0.0394425961671539
GO:0035250UDP-galactosyltransferase activity0.0401562837425331
GO:0045216intercellular junction assembly and maintenance0.0408122765299571
GO:0006687glycosphingolipid metabolic process0.0414172317562238
GO:0030148sphingolipid biosynthetic process0.0440698256137007
GO:0005856cytoskeleton0.0468734084861649
GO:0007028cytoplasm organization and biogenesis0.0468734084861649



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
neural tube8.60e-10056
neural rod8.60e-10056
future spinal cord8.60e-10056
neural keel8.60e-10056
regional part of nervous system7.10e-8753
regional part of brain7.10e-8753
central nervous system3.58e-7981
brain1.14e-7468
future brain1.14e-7468
nervous system9.89e-7189
neural plate2.41e-7082
presumptive neural plate2.41e-7082
neurectoderm8.68e-6786
brain grey matter2.35e-6234
gray matter2.35e-6234
telencephalon3.01e-6234
regional part of forebrain1.53e-6141
forebrain1.53e-6141
anterior neural tube1.53e-6141
future forebrain1.53e-6141
regional part of telencephalon3.57e-5432
ecto-epithelium3.96e-54104
cerebral hemisphere6.63e-5432
adult organism2.20e-52114
regional part of cerebral cortex4.67e-4422
structure with developmental contribution from neural crest6.07e-44132
pre-chordal neural plate1.85e-4361
neocortex4.18e-4220
posterior neural tube2.46e-3915
chordal neural plate2.46e-3915
cerebral cortex1.36e-3825
pallium1.36e-3825
ectoderm-derived structure4.64e-36171
ectoderm4.64e-36171
presumptive ectoderm4.64e-36171
brainstem6.70e-316
neural nucleus3.72e-269
nucleus of brain3.72e-269
organ system subdivision5.09e-26223
segmental subdivision of hindbrain6.37e-2612
hindbrain6.37e-2612
presumptive hindbrain6.37e-2612
tube1.66e-24192
segmental subdivision of nervous system7.84e-2413
gyrus8.98e-206
basal ganglion3.73e-199
nuclear complex of neuraxis3.73e-199
aggregate regional part of brain3.73e-199
collection of basal ganglia3.73e-199
cerebral subcortex3.73e-199
anatomical conduit3.42e-18240
telencephalic nucleus2.50e-177
spinal cord1.18e-163
dorsal region element1.18e-163
dorsum1.18e-163
medulla oblongata1.61e-163
myelencephalon1.61e-163
future myelencephalon1.61e-163
pons3.64e-163
occipital lobe1.19e-155
epithelium9.56e-14306
regional part of metencephalon1.16e-139
metencephalon1.16e-139
future metencephalon1.16e-139
organ part1.16e-13218
anatomical cluster1.21e-13373
cell layer1.53e-13309
temporal lobe2.56e-116
locus ceruleus2.59e-112
brainstem nucleus2.59e-112
hindbrain nucleus2.59e-112
corpus striatum3.17e-114
striatum3.17e-114
ventral part of telencephalon3.17e-114
future corpus striatum3.17e-114
middle temporal gyrus2.66e-102
multi-tissue structure1.51e-09342
limbic system1.62e-095
parietal lobe1.83e-095
frontal cortex1.93e-073
organ2.23e-07503
caudate-putamen4.05e-073
dorsal striatum4.05e-073


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)
MA0003.11.08123
MA0004.10.164226
MA0006.10.00959877
MA0007.10.340746
MA0009.10.295212
MA0014.10.928098
MA0017.10.597798
MA0019.10.100079
MA0024.10.631021
MA0025.10.398381
MA0027.11.79461
MA0028.10.0116229
MA0029.10.234549
MA0030.11.2023
MA0031.11.039
MA0038.10.0798193
MA0040.10.238542
MA0041.10.408255
MA0042.11.40245
MA0043.10.295444
MA0046.10.28722
MA0048.10.176175
MA0050.10.0389209
MA0051.10.268697
MA0052.10.241195
MA0055.11.23332
MA0056.10
MA0057.11.08855
MA0058.10.217702
MA0059.11.38385
MA0060.10.0347326
MA0061.10.971848
MA0063.10
MA0066.10.0800001
MA0067.10.553259
MA0068.10.690544
MA0069.11.41712
MA0070.10.276295
MA0071.10.496436
MA0072.10.273057
MA0073.115.8781
MA0074.10.267816
MA0076.10.0224905
MA0077.10.267535
MA0078.10.394373
MA0081.10.679275
MA0083.10.300765
MA0084.10.721137
MA0087.10.271301
MA0088.13.27374
MA0089.10
MA0090.10.790582
MA0091.11.48244
MA0092.10.312424
MA0093.10.13733
MA0095.10
MA0098.10
MA0100.10.0858032
MA0101.10.75277
MA0103.11.32309
MA0105.10.298475
MA0106.11.62838
MA0107.10.0681419
MA0108.21.63126
MA0109.10
MA0111.12.13428
MA0113.10.702295
MA0114.10.272528
MA0115.10.487485
MA0116.10.293865
MA0117.10.32334
MA0119.10.074899
MA0122.10.343167
MA0124.10.452592
MA0125.10.384032
MA0130.10
MA0131.10.134702
MA0132.10
MA0133.10
MA0135.11.53776
MA0136.10.0828349
MA0139.10.0477972
MA0140.10.226615
MA0141.10.410305
MA0142.15.46563
MA0143.12.98705
MA0144.10.125436
MA0145.12.57894
MA0146.10.0107116
MA0147.10.164952
MA0148.10.188509
MA0149.10.817013
MA0062.20.00069578
MA0035.20.0630244
MA0039.20.805374
MA0138.20.125638
MA0002.20.262615
MA0137.20.160933
MA0104.20.458521
MA0047.20.0926231
MA0112.22.42092
MA0065.21.75176
MA0150.10.0242915
MA0151.10
MA0152.10.0657794
MA0153.10.370648
MA0154.10.190637
MA0155.11.02948
MA0156.10.0128364
MA0157.10.894256
MA0158.10
MA0159.10.304415
MA0160.10.204102
MA0161.10
MA0162.10.0231338
MA0163.10.595802
MA0164.10.112235
MA0080.20.0499414
MA0018.20.325809
MA0099.20.0659162
MA0079.23.93054
MA0102.20.755388
MA0258.12.4979
MA0259.10.0810548
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

No analysis results for this cluster

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

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