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Coexpression cluster:C278: Difference between revisions

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991,0.692193,0.202638,0.000566703,0.00288363,0.166311,0.929517,0.0015616,0.312333,0.0580452,0.006642,0.017478,0.179236,0.0179382,0.317716,6.8221e-05,0.00355844,0.0111623
|tfbs_overrepresentation_for_novel_motifs=0.0680101,0.628883,0.16876,0.393245,0.966628,0.390269,0.536463,0.153041,0.599858,0.0492384,0.337185,0.0900888,1.01107,0.513306,0.248112,0.293993,0.185123,1.27982,0.301795,0.446435,0.168834,0.189261,0.0429735,0.241116,0.0210937,0.675858,1.07853,0.163422,0.256586,0.380627,0.126765,0.208225,0.215238,0.0861283,0.341247,1.47379,0.00493782,0.173798,1.5781,0.954606,0.78673,0.274682,0.107738,0.245261,0.162294,0.0824587,0.252715,0.580827,0.290618,0.12373,0.347783,0.562793,0.323039,0.259727,0.373267,0.0686071,1.35221,0.207058,0.254669,0.788489,0.235165,0.073311,0.14944,0.168459,0.0806363,0.148683,0.444327,0.768402,0.201596,0.621219,0.103891,0.44314,0.000320405,0.971609,0.0345002,0.65912,0.768163,2.13404,0.578811,0.0883502,0.897309,0.167826,0.0804887,0.86027,0.332069,0.184198,0.750316,0.506745,1.82101,0.860953,0.522821,0.311831,0.219125,1.10082,0.0429631,0.895964,1.38754,0.247685,0.122374,1.19762,1.58945,0.215435,0.243872,0.549584,0.438502,0.141289,0.177726,0.234986,0.438617,0.0358843,1.24974,0.241987,0.545796,0.635079,0.482063,0.181356,0.0194595,2.1932,0.451255,2.19014,0.957347,0.118792,0.684636,0.288769,0.577125,0.933171,0.244426,0.633055,0.398874,0.0191328,0.312344,0.305407,0.410414,1.492,0.533887,0.327439,0.121932,0.373503,0.497634,1.29861,0.910351,1.17719,1.35336,0.245272,1.39682,1.64521,0.134233,1.14349,0.502046,0.0492434,0.0594598,0.00589812,0.312627,1.3134,0.0731181,0.648552,0.111935,0.106005,0.0926062,0.0737724,0.465252,0.298975,0.577621,0.379866,0.463413,0.578093,0.198112,0.0714183,0.0221279
|tfbs_overrepresentation_for_novel_motifs=0.0680101,0.628883,0.16876,0.393245,0.966628,0.390269,0.536463,0.153041,0.599858,0.0492384,0.337185,0.0900888,1.01107,0.513306,0.248112,0.293993,0.185123,1.27982,0.301795,0.446435,0.168834,0.189261,0.0429735,0.241116,0.0210937,0.675858,1.07853,0.163422,0.256586,0.380627,0.126765,0.208225,0.215238,0.0861283,0.341247,1.47379,0.00493782,0.173798,1.5781,0.954606,0.78673,0.274682,0.107738,0.245261,0.162294,0.0824587,0.252715,0.580827,0.290618,0.12373,0.347783,0.562793,0.323039,0.259727,0.373267,0.0686071,1.35221,0.207058,0.254669,0.788489,0.235165,0.073311,0.14944,0.168459,0.0806363,0.148683,0.444327,0.768402,0.201596,0.621219,0.103891,0.44314,0.000320405,0.971609,0.0345002,0.65912,0.768163,2.13404,0.578811,0.0883502,0.897309,0.167826,0.0804887,0.86027,0.332069,0.184198,0.750316,0.506745,1.82101,0.860953,0.522821,0.311831,0.219125,1.10082,0.0429631,0.895964,1.38754,0.247685,0.122374,1.19762,1.58945,0.215435,0.243872,0.549584,0.438502,0.141289,0.177726,0.234986,0.438617,0.0358843,1.24974,0.241987,0.545796,0.635079,0.482063,0.181356,0.0194595,2.1932,0.451255,2.19014,0.957347,0.118792,0.684636,0.288769,0.577125,0.933171,0.244426,0.633055,0.398874,0.0191328,0.312344,0.305407,0.410414,1.492,0.533887,0.327439,0.121932,0.373503,0.497634,1.29861,0.910351,1.17719,1.35336,0.245272,1.39682,1.64521,0.134233,1.14349,0.502046,0.0492434,0.0594598,0.00589812,0.312627,1.3134,0.0731181,0.648552,0.111935,0.106005,0.0926062,0.0737724,0.465252,0.298975,0.577621,0.379866,0.463413,0.578093,0.198112,0.0714183,0.0221279
|tfbs_overrepresentation_jaspar=MA0003.1;0.00349298,MA0004.1;0.149807,MA0006.1;0.0418213,MA0007.1;0.314162,MA0009.1;0.282049,MA0014.1;0.0812748,MA0017.1;0.0615642,MA0019.1;0.308124,MA0024.1;0.209896,MA0025.1;0.383675,MA0027.1;1.77546,MA0028.1;0.00983297,MA0029.1;1.84937,MA0030.1;0.215031,MA0031.1;0.174316,MA0038.1;0.254626,MA0040.1;0.226506,MA0041.1;0.166866,MA0042.1;0.323094,MA0043.1;0.282278,MA0046.1;0.753137,MA0048.1;0.0855519,MA0050.1;0.324596,MA0051.1;0.0713589,MA0052.1;0.648779,MA0055.1;1.26698,MA0056.1;0,MA0057.1;0.210418,MA0058.1;0.0766141,MA0059.1;0.19517,MA0060.1;0.0286759,MA0061.1;0.311386,MA0063.1;0,MA0066.1;0.0732172,MA0067.1;0.537012,MA0068.1;0.819117,MA0069.1;0.746822,MA0070.1;0.728559,MA0071.1;0.212157,MA0072.1;0.260306,MA0073.1;3.56519,MA0074.1;0.248986,MA0076.1;0.0195703,MA0077.1;0.254892,MA0078.1;0.371676,MA0081.1;0.0759016,MA0083.1;0.287504,MA0084.1;0.703837,MA0087.1;0.258584,MA0088.1;0.0345497,MA0089.1;0,MA0090.1;0.240463,MA0091.1;1.88241,MA0092.1;0.287028,MA0093.1;0.0431902,MA0095.1;0,MA0098.1;0,MA0100.1;0.0787315,MA0101.1;0.449727,MA0103.1;0.108723,MA0105.1;0.166301,MA0106.1;1.05193,MA0107.1;0.253705,MA0108.2;0.172469,MA0109.1;0,MA0111.1;0.26112,MA0113.1;1.10452,MA0114.1;0.0546908,MA0115.1;0.471806,MA0116.1;0.261874,MA0117.1;0.309701,MA0119.1;0.576012,MA0122.1;0.329219,MA0124.1;0.437263,MA0125.1;0.36951,MA0130.1;0,MA0131.1;0.12559,MA0132.1;0,MA0133.1;0,MA0135.1;0.304312,MA0136.1;0.262713,MA0139.1;0.0866548,MA0140.1;0.459236,MA0141.1;0.192805,MA0142.1;0.155551,MA0143.1;1.10509,MA0144.1;0.210277,MA0145.1;0.548724,MA0146.1;0.257768,MA0147.1;0.0634182,MA0148.1;0.390676,MA0149.1;0.44056,MA0062.2;0.0443033,MA0035.2;0.208625,MA0039.2;0.132282,MA0138.2;0.11686,MA0002.2;0.229858,MA0137.2;0.0526133,MA0104.2;0.00777397,MA0047.2;0.288653,MA0112.2;0.183223,MA0065.2;0.0121981,MA0150.1;0.0212056,MA0151.1;0,MA0152.1;0.817398,MA0153.1;0.356306,MA0154.1;0.478907,MA0155.1;0.23489,MA0156.1;0.0537852,MA0157.1;0.432983,MA0158.1;0,MA0159.1;0.0201627,MA0160.1;0.187803,MA0161.1;0,MA0162.1;0.15238,MA0163.1;0.0152053,MA0164.1;0.103984,MA0080.2;0.253231,MA0018.2;0.0912146,MA0099.2;0.472777,MA0079.2;0.292951,MA0102.2;0.737926,MA0258.1;0.0967444,MA0259.1;0.0699433,MA0442.1;0
}}
}}

Revision as of 18:57, 22 January 2013


Full id: C278_amygdala_hippocampus_insula_medial_putamen_temporal_olfactory



Phase1 CAGE Peaks

Hg19::chr10:126694575..126694592,-p16@CTBP2
Hg19::chr11:134282221..134282236,-p6@B3GAT1
Hg19::chr12:123466296..123466326,+p9@ARL6IP4
Hg19::chr13:101712292..101712306,-p@chr13:101712292..101712306
-
Hg19::chr13:44721892..44721904,-p@chr13:44721892..44721904
-
Hg19::chr14:23983481..23983496,+p@chr14:23983481..23983496
+
Hg19::chr14:71905725..71905743,+p@chr14:71905725..71905743
+
Hg19::chr14:76241843..76241862,+p@chr14:76241843..76241862
+
Hg19::chr14:94640408..94640419,+p7@PPP4R4
Hg19::chr15:26147599..26147637,+p1@ENST00000557171
Hg19::chr15:77988462..77988479,-p15@LINGO1
Hg19::chr16:19183650..19183662,+p8@SYT17
Hg19::chr16:19183671..19183690,+p5@SYT17
Hg19::chr16:19183729..19183750,+p7@SYT17
Hg19::chr16:57980465..57980483,-p@chr16:57980465..57980483
-
Hg19::chr16:84002103..84002117,+p2@NECAB2
Hg19::chr17:1029026..1029035,-p37@ABR
Hg19::chr17:57604227..57604236,-p@chr17:57604227..57604236
-
Hg19::chr18:32402321..32402331,+p@chr18:32402321..32402331
+
Hg19::chr19:10506556..10506567,-p6@CDC37
Hg19::chr1:95975684..95975731,+p1@ENST00000432146
p1@ENST00000440116
p1@ENST00000456933
Hg19::chr22:39178758..39178776,-p2@DNAL4
Hg19::chr2:10508688..10508712,+p8@HPCAL1
Hg19::chr2:10508772..10508805,+p4@HPCAL1
Hg19::chr2:183387791..183387813,-p12@PDE1A
Hg19::chr2:242811874..242811904,+p1@CXXC11
Hg19::chr2:242814260..242814263,+p@chr2:242814260..242814263
+
Hg19::chr3:113023094..113023109,-p3@WDR52
Hg19::chr3:113023157..113023168,-p4@WDR52
Hg19::chr3:131756559..131756572,-p7@CPNE4
Hg19::chr3:131756595..131756614,-p4@CPNE4
Hg19::chr3:131756632..131756637,-p11@CPNE4
Hg19::chr3:131756644..131756651,-p13@CPNE4
Hg19::chr3:71777824..71777833,-p28@EIF4E3
Hg19::chr4:118735142..118735153,-p@chr4:118735142..118735153
-
Hg19::chr4:139230927..139230941,+p2@ENST00000510736
p2@ENST00000515282
Hg19::chr4:46391095..46391114,-p14@GABRA2
Hg19::chr6:76072731..76072770,-p8@FILIP1
Hg19::chr6:90272488..90272510,+p7@ANKRD6
Hg19::chr7:13141010..13141018,+p2@ENST00000443947
Hg19::chr7:29845734..29845742,+p16@WIPF3
Hg19::chr8:54752406..54752429,-p5@ATP6V1H
Hg19::chr8:89554843..89554848,+p2@ENST00000518631
Hg19::chr8:89554909..89554920,+p3@ENST00000518631
Hg19::chr9:13165461..13165485,-p13@MPDZ


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

p.valueFDRnGenesnPathwayName
1.85355118110106e-050.01173297897636974220Signalling by NGF (Reactome):REACT_11061



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
telencephalon4.41e-9134
cerebral hemisphere1.07e-8832
regional part of cerebral cortex2.74e-8622
brain grey matter3.16e-8334
gray matter3.16e-8334
regional part of forebrain6.93e-8241
forebrain6.93e-8241
anterior neural tube6.93e-8241
future forebrain6.93e-8241
regional part of telencephalon1.21e-8032
cerebral cortex6.46e-7625
pallium6.46e-7625
neocortex2.42e-7420
regional part of nervous system8.43e-7453
regional part of brain8.43e-7453
neural tube1.15e-6956
neural rod1.15e-6956
future spinal cord1.15e-6956
neural keel1.15e-6956
brain2.35e-6568
future brain2.35e-6568
central nervous system6.28e-6381
nervous system2.81e-5689
pre-chordal neural plate5.40e-5461
neural plate2.48e-4682
presumptive neural plate2.48e-4682
adult organism1.76e-44114
neurectoderm5.59e-4486
gyrus1.12e-376
ecto-epithelium1.33e-35104
limbic system6.43e-335
structure with developmental contribution from neural crest5.46e-32132
ectoderm-derived structure2.58e-27171
ectoderm2.58e-27171
presumptive ectoderm2.58e-27171
temporal lobe1.85e-236
organ system subdivision2.09e-21223
parietal lobe2.47e-205
frontal cortex7.74e-203
basal ganglion1.34e-179
nuclear complex of neuraxis1.34e-179
aggregate regional part of brain1.34e-179
collection of basal ganglia1.34e-179
cerebral subcortex1.34e-179
tube4.27e-17192
corpus striatum1.72e-144
striatum1.72e-144
ventral part of telencephalon1.72e-144
future corpus striatum1.72e-144
amygdala1.82e-142
Ammon's horn3.28e-142
lobe parts of cerebral cortex3.28e-142
hippocampal formation3.28e-142
limbic lobe3.28e-142
middle temporal gyrus4.26e-142
middle frontal gyrus1.19e-132
meninx2.24e-132
membrane organ2.24e-132
meningeal cluster2.24e-132
anatomical conduit1.11e-12240
organ part6.73e-12218
occipital lobe1.23e-115
neural nucleus3.93e-119
nucleus of brain3.93e-119
anatomical cluster1.05e-10373
caudate-putamen5.13e-093
dorsal striatum5.13e-093
pons5.80e-093
epithelium7.37e-09306
cell layer1.01e-08309
telencephalic nucleus1.69e-087
multi-tissue structure3.05e-08342
insula4.89e-081
olfactory region5.96e-081
primary subdivision of skull5.96e-081
cranium5.96e-081
neurocranium5.96e-081
chondrocranium5.96e-081
cartilaginous neurocranium5.96e-081
head paraxial mesoderm5.96e-081
nucleus accumbens8.84e-081
ventral striatum8.84e-081
paracentral gyrus1.22e-071
postcentral gyrus1.48e-071
occipital pole1.80e-071
pole of cerebral hemisphere1.80e-071
putamen2.04e-071
corpus callosum2.98e-071
central nervous system cell part cluster2.98e-071
axon tract2.98e-071
intercerebral commissure2.98e-071
dorsal telencephalic commissure2.98e-071
brain white matter2.98e-071
brain commissure2.98e-071
white matter2.98e-071
nervous system commissure2.98e-071
cerebral hemisphere white matter2.98e-071
dura mater3.17e-071
future meninx3.17e-071
ectomeninx3.17e-071


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)
MA0003.10.00349298
MA0004.10.149807
MA0006.10.0418213
MA0007.10.314162
MA0009.10.282049
MA0014.10.0812748
MA0017.10.0615642
MA0019.10.308124
MA0024.10.209896
MA0025.10.383675
MA0027.11.77546
MA0028.10.00983297
MA0029.11.84937
MA0030.10.215031
MA0031.10.174316
MA0038.10.254626
MA0040.10.226506
MA0041.10.166866
MA0042.10.323094
MA0043.10.282278
MA0046.10.753137
MA0048.10.0855519
MA0050.10.324596
MA0051.10.0713589
MA0052.10.648779
MA0055.11.26698
MA0056.10
MA0057.10.210418
MA0058.10.0766141
MA0059.10.19517
MA0060.10.0286759
MA0061.10.311386
MA0063.10
MA0066.10.0732172
MA0067.10.537012
MA0068.10.819117
MA0069.10.746822
MA0070.10.728559
MA0071.10.212157
MA0072.10.260306
MA0073.13.56519
MA0074.10.248986
MA0076.10.0195703
MA0077.10.254892
MA0078.10.371676
MA0081.10.0759016
MA0083.10.287504
MA0084.10.703837
MA0087.10.258584
MA0088.10.0345497
MA0089.10
MA0090.10.240463
MA0091.11.88241
MA0092.10.287028
MA0093.10.0431902
MA0095.10
MA0098.10
MA0100.10.0787315
MA0101.10.449727
MA0103.10.108723
MA0105.10.166301
MA0106.11.05193
MA0107.10.253705
MA0108.20.172469
MA0109.10
MA0111.10.26112
MA0113.11.10452
MA0114.10.0546908
MA0115.10.471806
MA0116.10.261874
MA0117.10.309701
MA0119.10.576012
MA0122.10.329219
MA0124.10.437263
MA0125.10.36951
MA0130.10
MA0131.10.12559
MA0132.10
MA0133.10
MA0135.10.304312
MA0136.10.262713
MA0139.10.0866548
MA0140.10.459236
MA0141.10.192805
MA0142.10.155551
MA0143.11.10509
MA0144.10.210277
MA0145.10.548724
MA0146.10.257768
MA0147.10.0634182
MA0148.10.390676
MA0149.10.44056
MA0062.20.0443033
MA0035.20.208625
MA0039.20.132282
MA0138.20.11686
MA0002.20.229858
MA0137.20.0526133
MA0104.20.00777397
MA0047.20.288653
MA0112.20.183223
MA0065.20.0121981
MA0150.10.0212056
MA0151.10
MA0152.10.817398
MA0153.10.356306
MA0154.10.478907
MA0155.10.23489
MA0156.10.0537852
MA0157.10.432983
MA0158.10
MA0159.10.0201627
MA0160.10.187803
MA0161.10
MA0162.10.15238
MA0163.10.0152053
MA0164.10.103984
MA0080.20.253231
MA0018.20.0912146
MA0099.20.472777
MA0079.20.292951
MA0102.20.737926
MA0258.10.0967444
MA0259.10.0699433
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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