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Coexpression cluster:C1418: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.603698,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.267027,0.075749,0.553339,0.707204,1.85338,0.650887,0.391663,0.415981,0.889639,0.892779,0.236034,0.127969,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,1.02557,0.186644,0.530785,0.92701,0.302275,0.640661,0.35719,0.316592,0.35388,0.585658,0.329602,0.248856,0.936389,0.513952,0.323162,0.390088,0.992846,0.468392,0.66382,0.542147,0.630853,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,1.75965,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.181326,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,0.661488,0.987239,0.776336,1.53398,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,2.31282,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,1.56093,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,0.683502,0.29379,0.661335,0.152397
|tfbs_overrepresentation_jaspar=MA0003.1;0.756372,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.0254709,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.213007,MA0056.1;0,MA0057.1;0.882847,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.737586,MA0061.1;0.671725,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;3.22865,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.720548,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;3.46565,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.419295,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;1.25994,MA0113.1;1.72264,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.865577,MA0117.1;1.07516,MA0119.1;1.96285,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.641617,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.0929059,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;2.58239,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.318517,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;1.18186,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.792956,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:55, 22 January 2013


Full id: C1418_insula_temporal_frontal_brain_occipital_paracentral_nucleus



Phase1 CAGE Peaks

Hg19::chr16:13901928..13901942,-p@chr16:13901928..13901942
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Hg19::chr1:208443938..208443947,-p@chr1:208443938..208443947
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Hg19::chr3:68040679..68040716,+p4@FAM19A1
Hg19::chr5:136535737..136535749,-p@chr5:136535737..136535749
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Hg19::chr5:136535760..136535778,-p@chr5:136535760..136535778
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Hg19::chr9:135036765..135036814,+p5@NTNG2


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:0046658anchored to plasma membrane0.0216310063372877
GO:0031225anchored to membrane0.0216310063372877
GO:0007409axonogenesis0.0464561149167197
GO:0048667neuron morphogenesis during differentiation0.0464561149167197
GO:0048812neurite morphogenesis0.0464561149167197
GO:0000904cellular morphogenesis during differentiation0.0464561149167197
GO:0048503GPI anchor binding0.0464561149167197
GO:0031175neurite development0.0464561149167197
GO:0048666neuron development0.0464561149167197
GO:0032990cell part morphogenesis0.0464561149167197
GO:0030030cell projection organization and biogenesis0.0464561149167197
GO:0048858cell projection morphogenesis0.0464561149167197
GO:0030182neuron differentiation0.0464561149167197
GO:0048699generation of neurons0.0470559676737943
GO:0035091phosphoinositide binding0.0470559676737943
GO:0022008neurogenesis0.0470559676737943



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 cerebral cortex1.09e-6822
neocortex3.50e-6520
cerebral hemisphere3.39e-6232
cerebral cortex1.67e-6025
pallium1.67e-6025
telencephalon1.71e-5834
regional part of forebrain1.57e-5441
forebrain1.57e-5441
anterior neural tube1.57e-5441
future forebrain1.57e-5441
regional part of telencephalon1.97e-5432
brain grey matter3.51e-5134
gray matter3.51e-5134
regional part of nervous system5.97e-4753
regional part of brain5.97e-4753
central nervous system3.76e-4581
brain1.98e-4468
future brain1.98e-4468
neural tube2.52e-4456
neural rod2.52e-4456
future spinal cord2.52e-4456
neural keel2.52e-4456
nervous system2.06e-4089
pre-chordal neural plate4.94e-3661
gyrus6.07e-356
adult organism5.32e-32114
neural plate1.66e-2982
presumptive neural plate1.66e-2982
neurectoderm5.20e-2886
ecto-epithelium1.10e-22104
structure with developmental contribution from neural crest9.15e-22132
ectoderm-derived structure9.10e-20171
ectoderm9.10e-20171
presumptive ectoderm9.10e-20171
temporal lobe1.94e-196
middle temporal gyrus7.43e-182
meninx2.85e-172
membrane organ2.85e-172
meningeal cluster2.85e-172
organ system subdivision5.90e-16223
parietal lobe9.07e-165
occipital lobe1.29e-155
limbic system1.92e-155
frontal cortex2.85e-123
tube6.50e-11192
insula3.74e-101
nucleus accumbens5.31e-101
ventral striatum5.31e-101
paracentral gyrus5.79e-101
postcentral gyrus7.50e-101
olfactory region9.70e-101
primary subdivision of skull9.70e-101
cranium9.70e-101
neurocranium9.70e-101
chondrocranium9.70e-101
cartilaginous neurocranium9.70e-101
head paraxial mesoderm9.70e-101
occipital pole1.06e-091
pole of cerebral hemisphere1.06e-091
dura mater2.46e-091
future meninx2.46e-091
ectomeninx2.46e-091
future dura mater2.46e-091
anatomical cluster3.94e-08373
anatomical conduit4.21e-08240
organ part4.52e-08218


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)
MA0003.10.756372
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.737586
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.13.22865
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.720548
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.13.46565
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.11.72264
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.11.96285
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0929059
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.12.58239
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.11.18186
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.792956
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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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