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Coexpression cluster:C256: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;5.52544e-06,MA0004.1;0.285642,MA0006.1;0.544565,MA0007.1;0.024623,MA0009.1;0.703091,MA0014.1;3.69883e-09,MA0017.1;0.124978,MA0019.1;0.262257,MA0024.1;0.183969,MA0025.1;0.350278,MA0027.1;1.73105,MA0028.1;0.00648135,MA0029.1;0.195946,MA0030.1;0.188804,MA0031.1;0.898074,MA0038.1;0.213125,MA0040.1;1.09698,MA0041.1;0.907724,MA0042.1;1.57338,MA0043.1;0.252653,MA0046.1;0.24494,MA0048.1;0.0103142,MA0050.1;0.109642,MA0051.1;0.79622,MA0052.1;1.10661,MA0055.1;0.0782628,MA0056.1;0,MA0057.1;0.308025,MA0058.1;0.0568651,MA0059.1;0.0561949,MA0060.1;0.0176478,MA0061.1;0.0300898,MA0063.1;0,MA0066.1;0.213568,MA0067.1;0.49981,MA0068.1;0.0707512,MA0069.1;0.679608,MA0070.1;0.234718,MA0071.1;0.0459331,MA0072.1;0.231695,MA0073.1;0.00021799,MA0074.1;0.207985,MA0076.1;0.0655073,MA0077.1;0.226543,MA0078.1;0.097239,MA0081.1;2.85582,MA0083.1;0.25765,MA0084.1;0.664025,MA0087.1;0.651017,MA0088.1;0.00303212,MA0089.1;0,MA0090.1;0.619096,MA0091.1;0.121304,MA0092.1;0.441881,MA0093.1;0.194773,MA0095.1;0,MA0098.1;0,MA0100.1;0.49318,MA0101.1;0.0312519,MA0103.1;0.318689,MA0105.1;0.00179314,MA0106.1;0.257854,MA0107.1;0.0959267,MA0108.2;0.14894,MA0109.1;0,MA0111.1;0.209449,MA0113.1;0.276654,MA0114.1;0.0365608,MA0115.1;0.436009,MA0116.1;0.041195,MA0117.1;0.27892,MA0119.1;0.274103,MA0122.1;0.297683,MA0124.1;0.402329,MA0125.1;0.336564,MA0130.1;0,MA0131.1;0.10574,MA0132.1;0,MA0133.1;0,MA0135.1;0.752104,MA0136.1;0.479857,MA0139.1;0.109977,MA0140.1;0.0451217,MA0141.1;0.302539,MA0142.1;0.133251,MA0143.1;0.27686,MA0144.1;0.611919,MA0145.1;0.025145,MA0146.1;5.53494e-05,MA0147.1;0.104091,MA0148.1;0.326148,MA0149.1;0.0422402,MA0062.2;0.00915808,MA0035.2;0.0449079,MA0039.2;6.5145e-06,MA0138.2;0.0978028,MA0002.2;0.0875896,MA0137.2;0.107881,MA0104.2;0.10248,MA0047.2;0.0694194,MA0112.2;0.00375503,MA0065.2;0.0275292,MA0150.1;0.360429,MA0151.1;0,MA0152.1;0.708941,MA0153.1;0.323801,MA0154.1;0.0975962,MA0155.1;0.0028753,MA0156.1;0.110132,MA0157.1;0.76104,MA0158.1;0,MA0159.1;0.0128504,MA0160.1;0.35201,MA0161.1;0,MA0162.1;1.43571e-05,MA0163.1;0.000511528,MA0164.1;1.02028,MA0080.2;1.11003,MA0018.2;0.0747401,MA0099.2;0.401694,MA0079.2;2.28063e-14,MA0102.2;0.697711,MA0258.1;0.13646,MA0259.1;0.560229,MA0442.1;0
}}
}}

Revision as of 18:52, 22 January 2013


Full id: C256_occipital_caudate_amygdala_medial_thalamus_hippocampus_medulla



Phase1 CAGE Peaks

Hg19::chr10:83635586..83635597,+p6@NRG3
Hg19::chr11:10529999..10530000,-p3@MIR4485
Hg19::chr12:48111295..48111297,-p@chr12:48111295..48111297
-
Hg19::chr12:53438340..53438344,+p@chr12:53438340..53438344
+
Hg19::chr13:110775905..110775918,+p1@LOC283485
Hg19::chr14:101313715..101313726,-p3@AK126659
Hg19::chr14:101314924..101314935,-p@chr14:101314924..101314935
-
Hg19::chr14:102551227..102551242,+p@chr14:102551227..102551242
+
Hg19::chr14:73570140..73570193,-p@chr14:73570140..73570193
-
Hg19::chr15:34260460..34260472,+p2@CHRM5
Hg19::chr15:34260686..34260710,+p1@CHRM5
Hg19::chr15:69019611..69019647,+p@chr15:69019611..69019647
+
Hg19::chr16:68750222..68750228,+p@chr16:68750222..68750228
+
Hg19::chr17:22023159..22023161,+p@chr17:22023159..22023161
+
Hg19::chr18:32400519..32400523,-p@chr18:32400519..32400523
-
Hg19::chr19:45298867..45298869,+p@chr19:45298867..45298869
+
Hg19::chr1:204580692..204580695,-p@chr1:204580692..204580695
-
Hg19::chr1:24645071..24645074,+p@chr1:24645071..24645074
+
Hg19::chr22:49283073..49283079,+p@chr22:49283073..49283079
+
Hg19::chr2:165410518..165410520,+p@chr2:165410518..165410520
+
Hg19::chr2:220348295..220348300,+p@chr2:220348295..220348300
+
Hg19::chr2:70951535..70951538,+p@chr2:70951535..70951538
+
Hg19::chr3:14873451..14873452,+p@chr3:14873451..14873452
+
Hg19::chr3:88650202..88650205,+p1@ENST00000468361
Hg19::chr4:88415555..88415573,+p@chr4:88415555..88415573
+
Hg19::chr4:88447806..88447810,+p@chr4:88447806..88447810
+
Hg19::chr5:134259812..134259816,+p3@MTND6P4
Hg19::chr5:134260393..134260413,+p@chr5:134260393..134260413
+
Hg19::chr5:134263450..134263463,+p2@MIR4461
Hg19::chr5:134263476..134263487,+p6@MIR4461
Hg19::chr6:121756901..121756912,+p4@GJA1
Hg19::chr6:2911513..2911514,+p@chr6:2911513..2911514
+
Hg19::chr7:103179905..103179918,-p4@RELN
Hg19::chr7:105516839..105516841,+p10@CDHR3
Hg19::chr8:104184270..104184280,-p2@ENST00000521102
Hg19::chr8:131961464..131961485,+p@chr8:131961464..131961485
+
Hg19::chr8:24774826..24774901,-p@chr8:24774826..24774901
-
Hg19::chr8:24775032..24775050,-p@chr8:24775032..24775050
-
Hg19::chr8:24775054..24775104,-p@chr8:24775054..24775104
-
Hg19::chr8:24775187..24775201,-p@chr8:24775187..24775201
-
Hg19::chr8:24775491..24775536,-p@chr8:24775491..24775536
-
Hg19::chr8:24810309..24810339,+p2@CU691685
Hg19::chr9:2157655..2157669,+p24@SMARCA2
Hg19::chrM:1604..1614,+p1@uc004cor.1
Hg19::chrM:5322..5344,-p6@AK000561
Hg19::chrM:5715..5730,-p11@AK000561
Hg19::chrX:101380689..101380700,+p4@TCEAL2
Hg19::chrX:102632720..102632761,+p8@NGFRAP1
Hg19::chrX:138724994..138725023,-p2@MCF2
Hg19::chrX:20135072..20135077,-p9@MAP7D2
Hg19::chrX:46618069..46618072,+p@chrX:46618069..46618072
+


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:0032989cellular structure morphogenesis0.000399668203536365
GO:0000902cell morphogenesis0.000399668203536365
GO:0031175neurite development0.000399668203536365
GO:0048666neuron development0.000445259638768424
GO:0032990cell part morphogenesis0.000563980050971357
GO:0048858cell projection morphogenesis0.000563980050971357
GO:0030030cell projection organization and biogenesis0.000563980050971357
GO:0030182neuron differentiation0.000563980050971357
GO:0048699generation of neurons0.000765924806671898
GO:0022008neurogenesis0.000873649736739441
GO:0001764neuron migration0.00091837531401086
GO:0007242intracellular signaling cascade0.00091837531401086
GO:0032501multicellular organismal process0.00125855994145845
GO:0009653anatomical structure morphogenesis0.00143788039807146
GO:0007275multicellular organismal development0.00157067795046963
GO:0048468cell development0.00244710526549635
GO:0010232vascular transport0.00490369231408565
GO:0048731system development0.00533642506746418
GO:0048667neuron morphogenesis during differentiation0.00533642506746418
GO:0048812neurite morphogenesis0.00533642506746418
GO:0000904cellular morphogenesis during differentiation0.00533642506746418
GO:0032502developmental process0.00533642506746418
GO:0050794regulation of cellular process0.00533642506746418
GO:0016264gap junction assembly0.00533642506746418
GO:0015867ATP transport0.00533642506746418
GO:0051503adenine nucleotide transport0.00533642506746418
GO:0015865purine nucleotide transport0.00533642506746418
GO:0045844positive regulation of striated muscle development0.00533642506746418
GO:0007197muscarinic acetylcholine receptor, adenylate cyclase inhibiting pathway0.00533642506746418
GO:0048869cellular developmental process0.00533642506746418
GO:0030154cell differentiation0.00533642506746418
GO:0007399nervous system development0.00533642506746418
GO:0009966regulation of signal transduction0.0067577507656406
GO:0050789regulation of biological process0.0067577507656406
GO:0048856anatomical structure development0.0067577507656406
GO:0006862nucleotide transport0.0067577507656406
GO:0030297transmembrane receptor protein tyrosine kinase activator activity0.0067577507656406
GO:0015872dopamine transport0.00793685771538271
GO:0005771multivesicular body0.00793685771538271
GO:0043403skeletal muscle regeneration0.00793685771538271
GO:0002070epithelial cell maturation0.00793685771538271
GO:0030971receptor tyrosine kinase binding0.00793685771538271
GO:0065007biological regulation0.00850290002631808
GO:0048265response to pain0.00850290002631808
GO:0005916fascia adherens0.00850290002631808
GO:0002064epithelial cell development0.00850290002631808
GO:0005243gap junction channel activity0.00850290002631808
GO:0045732positive regulation of protein catabolic process0.00850290002631808
GO:0021511spinal cord patterning0.00850290002631808
GO:0016477cell migration0.00900988650186093
GO:0009790embryonic development0.00900988650186093
GO:0022829wide pore channel activity0.00943243420928138
GO:0030296protein tyrosine kinase activator activity0.00943243420928138
GO:0035050embryonic heart tube development0.010231206359391
GO:0007512adult heart development0.010231206359391
GO:0007213acetylcholine receptor signaling, muscarinic pathway0.010231206359391
GO:0009896positive regulation of catabolic process0.010231206359391
GO:0048513organ development0.0109249402049422
GO:0009268response to pH0.0109249402049422
GO:0051057positive regulation of small GTPase mediated signal transduction0.0109249402049422
GO:0004981muscarinic acetylcholine receptor activity0.0109249402049422
GO:0001947heart looping0.01209107719632
GO:0021510spinal cord development0.0132199216909085
GO:0033555multicellular organismal response to stress0.014913734021112
GO:0051924regulation of calcium ion transport0.014913734021112
GO:0016358dendrite development0.014913734021112
GO:0030295protein kinase activator activity0.014913734021112
GO:0005887integral to plasma membrane0.0150330141389711
GO:0007165signal transduction0.0150330141389711
GO:0031226intrinsic to plasma membrane0.0150330141389711
GO:0005913cell-cell adherens junction0.0150330141389711
GO:0016202regulation of striated muscle development0.0150330141389711
GO:0007243protein kinase cascade0.01554022287202
GO:0007043intercellular junction assembly0.01554022287202
GO:0030879mammary gland development0.01554022287202
GO:0006928cell motility0.0156024026347067
GO:0051674localization of cell0.0156024026347067
GO:0003007heart morphogenesis0.0168575278318891
GO:0042246tissue regeneration0.0168575278318891
GO:0043269regulation of ion transport0.0172516267171345
GO:0042176regulation of protein catabolic process0.0172516267171345
GO:0045216intercellular junction assembly and maintenance0.0172516267171345
GO:0007193G-protein signaling, adenylate cyclase inhibiting pathway0.0172516267171345
GO:0031099regeneration0.0172516267171345
GO:0019209kinase activator activity0.0172516267171345
GO:0030054cell junction0.0172516267171345
GO:0007154cell communication0.0172516267171345
GO:0016043cellular component organization and biogenesis0.0176900902268137
GO:0030165PDZ domain binding0.0184888344915059
GO:0017124SH3 domain binding0.0184888344915059
GO:0015464acetylcholine receptor activity0.0191979659125002
GO:0051056regulation of small GTPase mediated signal transduction0.0196776083318331
GO:0042166acetylcholine binding0.0196776083318331
GO:0007028cytoplasm organization and biogenesis0.021233740315628
GO:0009894regulation of catabolic process0.0218833993021424
GO:0005922connexon complex0.0242466077980364
GO:0010001glial cell differentiation0.0248511060954488
GO:0005921gap junction0.0288236293168925
GO:0042063gliogenesis0.029902594608196
GO:0030855epithelial cell differentiation0.029902594608196
GO:0048589developmental growth0.030425799462554
GO:0007267cell-cell signaling0.0319381431203324
GO:0018108peptidyl-tyrosine phosphorylation0.0335238577028587
GO:0008016regulation of heart contraction0.0335238577028587
GO:0018212peptidyl-tyrosine modification0.0342602000701058
GO:0043176amine binding0.0342602000701058
GO:0004434inositol or phosphatidylinositol phosphodiesterase activity0.0342602000701058
GO:0048469cell maturation0.0342602000701058
GO:0004435phosphoinositide phospholipase C activity0.0342602000701058
GO:0048732gland development0.0345091178567572
GO:0003015heart process0.0345091178567572
GO:0014704intercalated disc0.0345091178567572
GO:0060047heart contraction0.0345091178567572
GO:0005769early endosome0.0356546550359624
GO:0001701in utero embryonic development0.036062220017993
GO:0005770late endosome0.036462611212125
GO:0008283cell proliferation0.0372426018765522
GO:0021700developmental maturation0.0372426018765522
GO:0005912adherens junction0.037622550838198
GO:0007411axon guidance0.0385236784114739
GO:0044459plasma membrane part0.0385236784114739
GO:0004629phospholipase C activity0.0387241888721976
GO:0051259protein oligomerization0.0417571008387655
GO:0002009morphogenesis of an epithelium0.0420840877689062
GO:0008227amine receptor activity0.0443797674482315
GO:0006915apoptosis0.0450017594557596
GO:0012501programmed cell death0.0453442917401657
GO:0007264small GTPase mediated signal transduction0.0461864129273724
GO:0016265death0.0488876038405213
GO:0008219cell death0.0488876038405213
GO:0006836neurotransmitter transport0.0492438315404021



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
regional part of nervous system2.39e-12853
regional part of brain2.39e-12853
neural tube5.44e-12856
neural rod5.44e-12856
future spinal cord5.44e-12856
neural keel5.44e-12856
brain8.31e-10368
future brain8.31e-10368
regional part of forebrain7.51e-9741
forebrain7.51e-9741
anterior neural tube7.51e-9741
future forebrain7.51e-9741
central nervous system2.45e-9081
brain grey matter9.27e-8834
gray matter9.27e-8834
telencephalon3.68e-8734
cerebral hemisphere7.92e-8632
neural plate1.31e-8582
presumptive neural plate1.31e-8582
neurectoderm2.46e-8186
nervous system8.88e-8189
regional part of telencephalon5.38e-7932
ecto-epithelium3.99e-66104
regional part of cerebral cortex6.90e-6422
adult organism8.34e-64114
pre-chordal neural plate1.66e-6361
cerebral cortex4.90e-5625
pallium4.90e-5625
neocortex5.34e-5520
structure with developmental contribution from neural crest1.35e-53132
ectoderm-derived structure3.50e-39171
ectoderm3.50e-39171
presumptive ectoderm3.50e-39171
neural nucleus1.13e-339
nucleus of brain1.13e-339
basal ganglion1.18e-339
nuclear complex of neuraxis1.18e-339
aggregate regional part of brain1.18e-339
collection of basal ganglia1.18e-339
cerebral subcortex1.18e-339
tube1.50e-32192
segmental subdivision of hindbrain7.20e-3112
hindbrain7.20e-3112
presumptive hindbrain7.20e-3112
posterior neural tube2.86e-3015
chordal neural plate2.86e-3015
organ system subdivision4.81e-30223
gyrus8.14e-296
segmental subdivision of nervous system2.24e-2813
brainstem3.45e-286
telencephalic nucleus1.12e-247
anatomical conduit1.52e-24240
limbic system2.10e-245
corpus striatum6.88e-204
striatum6.88e-204
ventral part of telencephalon6.88e-204
future corpus striatum6.88e-204
regional part of metencephalon8.50e-199
metencephalon8.50e-199
future metencephalon8.50e-199
organ part2.27e-18218
epithelium1.32e-17306
cell layer2.32e-17309
temporal lobe3.05e-176
caudate-putamen1.14e-153
dorsal striatum1.14e-153
parietal lobe2.06e-155
frontal cortex2.63e-153
pons5.17e-153
anatomical cluster5.39e-15373
medulla oblongata5.98e-153
myelencephalon5.98e-153
future myelencephalon5.98e-153
multi-tissue structure7.27e-15342
regional part of diencephalon1.19e-114
diencephalon2.31e-117
future diencephalon2.31e-117
middle frontal gyrus4.27e-112
Ammon's horn4.72e-112
lobe parts of cerebral cortex4.72e-112
hippocampal formation4.72e-112
limbic lobe4.72e-112
caudate nucleus4.96e-112
future caudate nucleus4.96e-112
middle temporal gyrus5.75e-112
locus ceruleus6.67e-112
brainstem nucleus6.67e-112
hindbrain nucleus6.67e-112
amygdala7.01e-112
dorsal plus ventral thalamus9.41e-112
globus pallidus9.41e-112
pallidum9.41e-112
thalamic complex9.41e-112
occipital lobe2.12e-095
organ2.75e-08503
cerebellum7.66e-086
rhombic lip7.66e-086
germ layer2.55e-07560
germ layer / neural crest2.55e-07560
embryonic tissue2.55e-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)
MA0003.15.52544e-06
MA0004.10.285642
MA0006.10.544565
MA0007.10.024623
MA0009.10.703091
MA0014.13.69883e-09
MA0017.10.124978
MA0019.10.262257
MA0024.10.183969
MA0025.10.350278
MA0027.11.73105
MA0028.10.00648135
MA0029.10.195946
MA0030.10.188804
MA0031.10.898074
MA0038.10.213125
MA0040.11.09698
MA0041.10.907724
MA0042.11.57338
MA0043.10.252653
MA0046.10.24494
MA0048.10.0103142
MA0050.10.109642
MA0051.10.79622
MA0052.11.10661
MA0055.10.0782628
MA0056.10
MA0057.10.308025
MA0058.10.0568651
MA0059.10.0561949
MA0060.10.0176478
MA0061.10.0300898
MA0063.10
MA0066.10.213568
MA0067.10.49981
MA0068.10.0707512
MA0069.10.679608
MA0070.10.234718
MA0071.10.0459331
MA0072.10.231695
MA0073.10.00021799
MA0074.10.207985
MA0076.10.0655073
MA0077.10.226543
MA0078.10.097239
MA0081.12.85582
MA0083.10.25765
MA0084.10.664025
MA0087.10.651017
MA0088.10.00303212
MA0089.10
MA0090.10.619096
MA0091.10.121304
MA0092.10.441881
MA0093.10.194773
MA0095.10
MA0098.10
MA0100.10.49318
MA0101.10.0312519
MA0103.10.318689
MA0105.10.00179314
MA0106.10.257854
MA0107.10.0959267
MA0108.20.14894
MA0109.10
MA0111.10.209449
MA0113.10.276654
MA0114.10.0365608
MA0115.10.436009
MA0116.10.041195
MA0117.10.27892
MA0119.10.274103
MA0122.10.297683
MA0124.10.402329
MA0125.10.336564
MA0130.10
MA0131.10.10574
MA0132.10
MA0133.10
MA0135.10.752104
MA0136.10.479857
MA0139.10.109977
MA0140.10.0451217
MA0141.10.302539
MA0142.10.133251
MA0143.10.27686
MA0144.10.611919
MA0145.10.025145
MA0146.15.53494e-05
MA0147.10.104091
MA0148.10.326148
MA0149.10.0422402
MA0062.20.00915808
MA0035.20.0449079
MA0039.26.5145e-06
MA0138.20.0978028
MA0002.20.0875896
MA0137.20.107881
MA0104.20.10248
MA0047.20.0694194
MA0112.20.00375503
MA0065.20.0275292
MA0150.10.360429
MA0151.10
MA0152.10.708941
MA0153.10.323801
MA0154.10.0975962
MA0155.10.0028753
MA0156.10.110132
MA0157.10.76104
MA0158.10
MA0159.10.0128504
MA0160.10.35201
MA0161.10
MA0162.11.43571e-05
MA0163.10.000511528
MA0164.11.02028
MA0080.21.11003
MA0018.20.0747401
MA0099.20.401694
MA0079.22.28063e-14
MA0102.20.697711
MA0258.10.13646
MA0259.10.560229
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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