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Coexpression cluster:C1304: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,0.436508,0.58616,1.80086,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,1.60251,0.236034,0.800617,0.436569,0.29639,0.576478,1.00694,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.640661,0.35719,0.0334022,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,0.154075,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,1.04504,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.594475,0.192925,0.84426,2.10892,2.08653,0.240887,0.86037,1.63739,0.272514,1.10535,0.0481066,0.398737,0.181871,0.771626,1.71797,2.97901,1.07807,0.94406,0.83374,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,1.65434,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,1.94435,0.683502,0.29379,1.58953,0.0115686
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,0.436508,0.58616,1.80086,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,1.60251,0.236034,0.800617,0.436569,0.29639,0.576478,1.00694,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.640661,0.35719,0.0334022,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,0.154075,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,1.04504,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.594475,0.192925,0.84426,2.10892,2.08653,0.240887,0.86037,1.63739,0.272514,1.10535,0.0481066,0.398737,0.181871,0.771626,1.71797,2.97901,1.07807,0.94406,0.83374,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,1.65434,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,1.94435,0.683502,0.29379,1.58953,0.0115686
|tfbs_overrepresentation_jaspar=MA0003.1;0.026277,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;2.15903,MA0031.1;2.02362,MA0038.1;0.665566,MA0040.1;2.19519,MA0041.1;0.578072,MA0042.1;1.3446,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;1.34656,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00076337,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;0.32124,MA0089.1;0,MA0090.1;0.490736,MA0091.1;1.37996,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;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,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;1.61362,MA0139.1;1.19942,MA0140.1;0.622527,MA0141.1;1.15452,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.093337,MA0147.1;0.327615,MA0148.1;1.42897,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.00570825,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;1.21643,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.0961854,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;0.113377,MA0164.1;0.738243,MA0080.2;1.80563,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.000444266,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:50, 22 January 2013


Full id: C1304_pons_medial_frontal_paracentral_hippocampus_nucleus_insula



Phase1 CAGE Peaks

Hg19::chr10:134760770..134760781,-p@chr10:134760770..134760781
-
Hg19::chr16:47920797..47920838,-p1@uc002eex.1
Hg19::chr3:120628150..120628164,+p4@STXBP5L
Hg19::chr4:86068867..86068880,+p@chr4:86068867..86068880
+
Hg19::chr4:86068886..86068893,+p@chr4:86068886..86068893
+
Hg19::chrX:85969610..85969619,+p4@DACH2


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

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
neural tube1.15e-10656
neural rod1.15e-10656
future spinal cord1.15e-10656
neural keel1.15e-10656
regional part of nervous system7.03e-9553
regional part of brain7.03e-9553
central nervous system7.37e-8481
brain7.78e-8168
future brain7.78e-8168
regional part of forebrain7.18e-7741
forebrain7.18e-7741
anterior neural tube7.18e-7741
future forebrain7.18e-7741
neural plate5.99e-7582
presumptive neural plate5.99e-7582
nervous system6.49e-7589
telencephalon1.17e-7334
brain grey matter1.57e-7334
gray matter1.57e-7334
neurectoderm3.70e-7186
cerebral hemisphere4.50e-6632
regional part of telencephalon1.25e-6532
adult organism5.60e-59114
ecto-epithelium1.14e-57104
pre-chordal neural plate6.30e-5461
regional part of cerebral cortex1.62e-5022
structure with developmental contribution from neural crest1.29e-46132
cerebral cortex2.95e-4425
pallium2.95e-4425
neocortex2.79e-4220
ectoderm-derived structure4.65e-38171
ectoderm4.65e-38171
presumptive ectoderm4.65e-38171
neural nucleus3.22e-329
nucleus of brain3.22e-329
posterior neural tube3.40e-2915
chordal neural plate3.40e-2915
gyrus4.10e-296
organ system subdivision2.04e-27223
tube3.36e-26192
basal ganglion4.75e-259
nuclear complex of neuraxis4.75e-259
aggregate regional part of brain4.75e-259
collection of basal ganglia4.75e-259
cerebral subcortex4.75e-259
telencephalic nucleus7.50e-247
brainstem6.59e-206
corpus striatum6.62e-204
striatum6.62e-204
ventral part of telencephalon6.62e-204
future corpus striatum6.62e-204
anatomical conduit1.87e-19240
segmental subdivision of hindbrain2.44e-1812
hindbrain2.44e-1812
presumptive hindbrain2.44e-1812
segmental subdivision of nervous system7.38e-1713
limbic system3.61e-165
frontal cortex2.10e-153
caudate-putamen3.74e-153
dorsal striatum3.74e-153
pons4.98e-153
epithelium1.21e-14306
cell layer1.99e-14309
spinal cord2.25e-143
dorsal region element2.25e-143
dorsum2.25e-143
anatomical cluster2.66e-14373
organ part3.76e-14218
regional part of metencephalon8.76e-139
metencephalon8.76e-139
future metencephalon8.76e-139
temporal lobe2.07e-116
Ammon's horn7.23e-112
lobe parts of cerebral cortex7.23e-112
hippocampal formation7.23e-112
limbic lobe7.23e-112
middle temporal gyrus8.36e-112
middle frontal gyrus1.01e-102
caudate nucleus1.42e-102
future caudate nucleus1.42e-102
multi-tissue structure2.11e-10342
locus ceruleus3.18e-102
brainstem nucleus3.18e-102
hindbrain nucleus3.18e-102
parietal lobe2.37e-095
occipital lobe4.39e-095
organ9.30e-08503
medulla oblongata2.25e-073
myelencephalon2.25e-073
future myelencephalon2.25e-073
germ layer8.98e-07560
germ layer / neural crest8.98e-07560
embryonic tissue8.98e-07560
presumptive structure8.98e-07560
germ layer / neural crest derived structure8.98e-07560
epiblast (generic)8.98e-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)
MA0003.10.026277
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
MA0030.12.15903
MA0031.12.02362
MA0038.10.665566
MA0040.12.19519
MA0041.10.578072
MA0042.11.3446
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.11.61362
MA0139.11.19942
MA0140.10.622527
MA0141.11.15452
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.093337
MA0147.10.327615
MA0148.11.42897
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.11.21643
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.113377
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.20.000444266
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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