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Coexpression cluster:C552: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.47731,0.176447,0.152819,0.258928,0.125522,0.25764,0.318839,0.814765,0.058273,0.654939,0.234283,0.934824,0.156166,0.309388,0.393521,0.431887,0.511522,0.309105,0.171822,0.152073,0.464958,0.179594,0.701134,0.775685,0.542899,0.374311,0.131361,0.249905,0.127478,0.0271182,0.217756,0.544857,1.94013,0.363901,0.340569,2.27421,0.33558,0.258546,0.622505,1.59325,0.103604,0.205653,0.588492,0.391064,0.108627,0.173971,0.319738,0.226038,0.18831,0.12756,0.386472,0.329494,0.193889,0.615394,0.758742,0.311792,0.407898,0.2852,0.274137,0.284391,0.582323,0.321692,0.212582,0.48664,0.336598,1.15514,0.843028,1.20113,0.535417,1.04233,0.570382,0.22329,0.0158491,0.756844,0.0383048,0.135657,0.0291633,0.471562,0.532468,0.18023,0.177931,0.48568,0.336303,1.74738,0.70821,0.00751148,0.0112665,0.263815,0.408949,1.29895,0.932961,0.68283,0.560183,0.571383,0.12599,0.0858933,0.385004,0.599297,0.412954,0.229879,0.626127,0.555021,0.594155,1.28107,0.445845,0.230832,0.500571,0.306566,0.18443,0.370056,0.160439,0.591605,0.149112,0.241506,0.886618,0.681552,0.00168014,0.216858,0.453946,0.977584,0.748992,1.0486,0.255485,0.345739,0.993708,0.472239,0.313614,0.564749,0.78949,0.291925,0.683478,0.627156,0.803201,0.342946,0.945426,0.249246,0.611533,0.698255,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.278424,0.432737,1.59165,0.203207,0.0770919,0.063941,0.00537053,0.683836,0.201134,0.321292,1.07219,0.394947,0.373254,0.543,0.493594,0.867287,0.66649,0.531753,0.499061,3.01774,0.335644,0.24839,0.317742,0.00560829
|tfbs_overrepresentation_for_novel_motifs=0.47731,0.176447,0.152819,0.258928,0.125522,0.25764,0.318839,0.814765,0.058273,0.654939,0.234283,0.934824,0.156166,0.309388,0.393521,0.431887,0.511522,0.309105,0.171822,0.152073,0.464958,0.179594,0.701134,0.775685,0.542899,0.374311,0.131361,0.249905,0.127478,0.0271182,0.217756,0.544857,1.94013,0.363901,0.340569,2.27421,0.33558,0.258546,0.622505,1.59325,0.103604,0.205653,0.588492,0.391064,0.108627,0.173971,0.319738,0.226038,0.18831,0.12756,0.386472,0.329494,0.193889,0.615394,0.758742,0.311792,0.407898,0.2852,0.274137,0.284391,0.582323,0.321692,0.212582,0.48664,0.336598,1.15514,0.843028,1.20113,0.535417,1.04233,0.570382,0.22329,0.0158491,0.756844,0.0383048,0.135657,0.0291633,0.471562,0.532468,0.18023,0.177931,0.48568,0.336303,1.74738,0.70821,0.00751148,0.0112665,0.263815,0.408949,1.29895,0.932961,0.68283,0.560183,0.571383,0.12599,0.0858933,0.385004,0.599297,0.412954,0.229879,0.626127,0.555021,0.594155,1.28107,0.445845,0.230832,0.500571,0.306566,0.18443,0.370056,0.160439,0.591605,0.149112,0.241506,0.886618,0.681552,0.00168014,0.216858,0.453946,0.977584,0.748992,1.0486,0.255485,0.345739,0.993708,0.472239,0.313614,0.564749,0.78949,0.291925,0.683478,0.627156,0.803201,0.342946,0.945426,0.249246,0.611533,0.698255,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.278424,0.432737,1.59165,0.203207,0.0770919,0.063941,0.00537053,0.683836,0.201134,0.321292,1.07219,0.394947,0.373254,0.543,0.493594,0.867287,0.66649,0.531753,0.499061,3.01774,0.335644,0.24839,0.317742,0.00560829
|tfbs_overrepresentation_jaspar=MA0003.1;0.000203219,MA0004.1;0.238283,MA0006.1;0.124371,MA0007.1;0.223897,MA0009.1;0.644692,MA0014.1;0.024058,MA0017.1;0.45828,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.134741,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;2.00914,MA0042.1;0.646075,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.0786451,MA0050.1;0.228625,MA0051.1;0.317617,MA0052.1;0.574006,MA0055.1;0.0967754,MA0056.1;0,MA0057.1;0.0158853,MA0058.1;0.167587,MA0059.1;0.166682,MA0060.1;0.0584466,MA0061.1;0.0461955,MA0063.1;0,MA0066.1;0.321498,MA0067.1;0.948938,MA0068.1;0.128042,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;0.616162,MA0073.1;0.368378,MA0074.1;0.316991,MA0076.1;0.178863,MA0077.1;0.608956,MA0078.1;0.402443,MA0081.1;0.499456,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.0965118,MA0089.1;0,MA0090.1;0.189305,MA0091.1;0.240316,MA0092.1;0.211423,MA0093.1;0.397767,MA0095.1;0,MA0098.1;0,MA0100.1;0.332778,MA0101.1;0.403202,MA0103.1;0.377626,MA0105.1;0.0129929,MA0106.1;0.355999,MA0107.1;0.0842574,MA0108.2;0.492699,MA0109.1;0,MA0111.1;0.578093,MA0113.1;0.968027,MA0114.1;0.278245,MA0115.1;0.874839,MA0116.1;0.0861811,MA0117.1;0.680135,MA0119.1;0.471628,MA0122.1;0.70466,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;0.418384,MA0132.1;0,MA0133.1;0,MA0135.1;0.673296,MA0136.1;0.327047,MA0139.1;0.159457,MA0140.1;0.286995,MA0141.1;0.165463,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.0738381,MA0145.1;0.23881,MA0146.1;0.0055415,MA0147.1;0.0881384,MA0148.1;1.31921,MA0149.1;0.279141,MA0062.2;0.168482,MA0035.2;0.286421,MA0039.2;0.0116984,MA0138.2;0.403517,MA0002.2;0.196222,MA0137.2;0.138998,MA0104.2;0.0580852,MA0047.2;0.914023,MA0112.2;0.22067,MA0065.2;0.667633,MA0150.1;0.185024,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;0.0124644,MA0155.1;0.204406,MA0156.1;0.140505,MA0157.1;0.442323,MA0158.1;0,MA0159.1;0.0884959,MA0160.1;0.26995,MA0161.1;0,MA0162.1;0.0005964,MA0163.1;0.00897585,MA0164.1;0.380804,MA0080.2;0.397909,MA0018.2;0.357181,MA0099.2;0.292649,MA0079.2;7.87875e-05,MA0102.2;1.16862,MA0258.1;0.242841,MA0259.1;0.0929051,MA0442.1;0
}}
}}

Revision as of 19:15, 22 January 2013


Full id: C552_medial_temporal_occipital_parietal_duodenum_brain_spinal



Phase1 CAGE Peaks

Hg19::chr10:105048252..105048262,+p@chr10:105048252..105048262
+
Hg19::chr10:105048347..105048358,+p@chr10:105048347..105048358
+
Hg19::chr11:132289875..132289896,-p12@OPCML
Hg19::chr16:7568144..7568155,+p@chr16:7568144..7568155
+
Hg19::chr17:44039779..44039792,+p6@MAPT
Hg19::chr17:44068857..44068869,+p8@MAPT
Hg19::chr2:149633261..149633270,+p1@AB384491
Hg19::chr2:50148868..50148876,-p32@NRXN1
Hg19::chr2:55253343..55253360,-p29@RTN4
Hg19::chr3:286287..286329,+p@chr3:286287..286329
+
Hg19::chr3:383640..383650,+p@chr3:383640..383650
+
Hg19::chr5:71482490..71482501,+p@chr5:71482490..71482501
+
Hg19::chr5:71482533..71482549,+p@chr5:71482533..71482549
+
Hg19::chr5:71489693..71489706,+p@chr5:71489693..71489706
+
Hg19::chr8:80567211..80567218,+p9@STMN2
Hg19::chr9:111911992..111912002,-p@chr9:111911992..111912002
-


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:0030516regulation of axon extension0.00010362994502982
GO:0030182neuron differentiation0.00010362994502982
GO:0048675axon extension0.00010362994502982
GO:0030426growth cone0.00010362994502982
GO:0030427site of polarized growth0.00010362994502982
GO:0048699generation of neurons0.00010362994502982
GO:0022008neurogenesis0.000112726089605561
GO:0050770regulation of axonogenesis0.000123735069240019
GO:0050767regulation of neurogenesis0.000237741650507623
GO:0007399nervous system development0.00158975368646609
GO:0007409axonogenesis0.00166359731717786
GO:0048667neuron morphogenesis during differentiation0.00166359731717786
GO:0048812neurite morphogenesis0.00166359731717786
GO:0000904cellular morphogenesis during differentiation0.00170318642141137
GO:0031175neurite development0.00182484678637508
GO:0048666neuron development0.00222579120033241
GO:0045298tubulin complex0.00304731298129318
GO:0032990cell part morphogenesis0.0031203738849544
GO:0048858cell projection morphogenesis0.0031203738849544
GO:0030030cell projection organization and biogenesis0.0031203738849544
GO:0019987negative regulation of anti-apoptosis0.00347582725292053
GO:0030517negative regulation of axon extension0.00347582725292053
GO:0048468cell development0.00347582725292053
GO:0050793regulation of developmental process0.00347582725292053
GO:0042995cell projection0.00575468023354051
GO:0045773positive regulation of axon extension0.00575468023354051
GO:0050771negative regulation of axonogenesis0.00575468023354051
GO:0048731system development0.00615746870355665
GO:0031116positive regulation of microtubule polymerization0.0062504053506897
GO:0031112positive regulation of microtubule polymerization or depolymerization0.00668206759859369
GO:0031113regulation of microtubule polymerization0.00668206759859369
GO:0005515protein binding0.00719152808698763
GO:0048869cellular developmental process0.00720625871783252
GO:0030154cell differentiation0.00720625871783252
GO:0046785microtubule polymerization0.00739713234206427
GO:0008038neuron recognition0.00791035634833841
GO:0050768negative regulation of neurogenesis0.00795198723378637
GO:0045767regulation of anti-apoptosis0.00795198723378637
GO:0048856anatomical structure development0.00795198723378637
GO:0050772positive regulation of axonogenesis0.00795198723378637
GO:0000902cell morphogenesis0.00795198723378637
GO:0032989cellular structure morphogenesis0.00795198723378637
GO:0016020membrane0.00795198723378637
GO:0051130positive regulation of cellular component organization and biogenesis0.00805275855365829
GO:0004985opioid receptor activity0.00805275855365829
GO:0050769positive regulation of neurogenesis0.00900202403800668
GO:0007275multicellular organismal development0.0104480426339578
GO:0017124SH3 domain binding0.0107811353522219
GO:0007026negative regulation of microtubule depolymerization0.0113835384307388
GO:0031114regulation of microtubule depolymerization0.0113835384307388
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0114425685972422
GO:0007019microtubule depolymerization0.0114425685972422
GO:0031110regulation of microtubule polymerization or depolymerization0.0138883244812153
GO:0008034lipoprotein binding0.0138883244812153
GO:0031109microtubule polymerization or depolymerization0.0150437531143522
GO:0030424axon0.0156967109218176
GO:0008037cell recognition0.0172315456118835
GO:0051261protein depolymerization0.020489944257951
GO:0008017microtubule binding0.0214525192020646
GO:0022610biological adhesion0.0216605349071122
GO:0007155cell adhesion0.0216605349071122
GO:0051129negative regulation of cellular component organization and biogenesis0.0216605349071122
GO:0030176integral to endoplasmic reticulum membrane0.0217253746280847
GO:0032502developmental process0.0225500834866176
GO:0030334regulation of cell migration0.0235007884009187
GO:0009653anatomical structure morphogenesis0.0235007884009187
GO:0031227intrinsic to endoplasmic reticulum membrane0.0235007884009187
GO:0015631tubulin binding0.0254237655144738
GO:0051094positive regulation of developmental process0.0254277678098717
GO:0051270regulation of cell motility0.0254316124385206
GO:0048523negative regulation of cellular process0.0257941112672204
GO:0040012regulation of locomotion0.0257941112672204
GO:0040011locomotion0.0257941112672204
GO:0048519negative regulation of biological process0.0264757184329733
GO:0051093negative regulation of developmental process0.0264757184329733
GO:0043005neuron projection0.0272872935115342
GO:0032501multicellular organismal process0.0272872935115342
GO:0005200structural constituent of cytoskeleton0.0280891153272492
GO:0051258protein polymerization0.0316265304462711
GO:0051128regulation of cellular component organization and biogenesis0.0321914258461296
GO:0000226microtubule cytoskeleton organization and biogenesis0.0324260624446285
GO:0051248negative regulation of protein metabolic process0.0326548287373963
GO:0048503GPI anchor binding0.038874450927321
GO:0019904protein domain specific binding0.038874450927321
GO:0031301integral to organelle membrane0.042017371296162
GO:0001653peptide receptor activity0.0436863081765911
GO:0008528peptide receptor activity, G-protein coupled0.0436863081765911
GO:0031300intrinsic to organelle membrane0.0443467218518709
GO:0006916anti-apoptosis0.0489890794507065



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 tube6.90e-9656
neural rod6.90e-9656
future spinal cord6.90e-9656
neural keel6.90e-9656
central nervous system4.88e-8981
regional part of nervous system2.39e-8653
regional part of brain2.39e-8653
nervous system9.15e-8389
brain2.15e-7668
future brain2.15e-7668
regional part of forebrain2.87e-7441
forebrain2.87e-7441
anterior neural tube2.87e-7441
future forebrain2.87e-7441
brain grey matter8.35e-7434
gray matter8.35e-7434
telencephalon1.91e-7334
cerebral hemisphere1.08e-6732
regional part of telencephalon1.90e-6732
neural plate5.99e-6682
presumptive neural plate5.99e-6682
regional part of cerebral cortex4.26e-6522
neurectoderm1.88e-6286
neocortex3.33e-5820
cerebral cortex6.25e-5725
pallium6.25e-5725
ecto-epithelium1.19e-52104
pre-chordal neural plate6.74e-5161
adult organism2.04e-42114
ectoderm-derived structure2.37e-42171
ectoderm2.37e-42171
presumptive ectoderm2.37e-42171
structure with developmental contribution from neural crest1.43e-39132
organ system subdivision1.26e-31223
tube1.29e-22192
gyrus8.96e-226
posterior neural tube1.24e-2115
chordal neural plate1.24e-2115
temporal lobe1.96e-186
parietal lobe2.62e-185
basal ganglion6.58e-189
nuclear complex of neuraxis6.58e-189
aggregate regional part of brain6.58e-189
collection of basal ganglia6.58e-189
cerebral subcortex6.58e-189
neural nucleus6.75e-189
nucleus of brain6.75e-189
limbic system7.34e-185
anatomical conduit3.95e-16240
anatomical cluster2.18e-15373
brainstem4.35e-146
segmental subdivision of hindbrain2.22e-1312
hindbrain2.22e-1312
presumptive hindbrain2.22e-1312
segmental subdivision of nervous system2.84e-1213
organ part3.24e-12218
epithelium3.85e-12306
occipital lobe4.42e-125
telencephalic nucleus5.26e-127
cell layer6.32e-12309
frontal cortex1.04e-113
spinal cord1.49e-113
dorsal region element1.49e-113
dorsum1.49e-113
pons3.73e-113
regional part of metencephalon8.80e-109
metencephalon8.80e-109
future metencephalon8.80e-109
middle frontal gyrus1.20e-082
middle temporal gyrus1.39e-082
Ammon's horn1.55e-082
lobe parts of cerebral cortex1.55e-082
hippocampal formation1.55e-082
limbic lobe1.55e-082
corpus striatum1.80e-084
striatum1.80e-084
ventral part of telencephalon1.80e-084
future corpus striatum1.80e-084
multi-tissue structure2.13e-08342
amygdala4.12e-082
locus ceruleus4.27e-082
brainstem nucleus4.27e-082
hindbrain nucleus4.27e-082
germ layer5.63e-07560
germ layer / neural crest5.63e-07560
embryonic tissue5.63e-07560
presumptive structure5.63e-07560
germ layer / neural crest derived structure5.63e-07560
epiblast (generic)5.63e-07560
embryonic structure7.64e-07564


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)
MA0003.10.000203219
MA0004.10.238283
MA0006.10.124371
MA0007.10.223897
MA0009.10.644692
MA0014.10.024058
MA0017.10.45828
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.12.00914
MA0042.10.646075
MA0043.10.644989
MA0046.10.634468
MA0048.10.0786451
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.0967754
MA0056.10
MA0057.10.0158853
MA0058.10.167587
MA0059.10.166682
MA0060.10.0584466
MA0061.10.0461955
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.10.128042
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.368378
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.499456
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.0965118
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.10.211423
MA0093.10.397767
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.403202
MA0103.10.377626
MA0105.10.0129929
MA0106.10.355999
MA0107.10.0842574
MA0108.20.492699
MA0109.10
MA0111.10.578093
MA0113.10.968027
MA0114.10.278245
MA0115.10.874839
MA0116.10.0861811
MA0117.10.680135
MA0119.10.471628
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.10.159457
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.0738381
MA0145.10.23881
MA0146.10.0055415
MA0147.10.0881384
MA0148.11.31921
MA0149.10.279141
MA0062.20.168482
MA0035.20.286421
MA0039.20.0116984
MA0138.20.403517
MA0002.20.196222
MA0137.20.138998
MA0104.20.0580852
MA0047.20.914023
MA0112.20.22067
MA0065.20.667633
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.0124644
MA0155.10.204406
MA0156.10.140505
MA0157.10.442323
MA0158.10
MA0159.10.0884959
MA0160.10.26995
MA0161.10
MA0162.10.0005964
MA0163.10.00897585
MA0164.10.380804
MA0080.20.397909
MA0018.20.357181
MA0099.20.292649
MA0079.27.87875e-05
MA0102.21.16862
MA0258.10.242841
MA0259.10.0929051
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

This analysis result is provided for C0 - C305 clusters.

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