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Coexpression cluster:C1416: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,0.436508,1.43205,1.01854,0.584466,0.662701,0.269608,1.35335,0.262261,0.553339,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.127969,0.436569,0.6169,0.576478,1.00694,0.483957,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,0.316592,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,1.6253,1.01199,0.354447,0.468392,0.66382,0.542147,1.56014,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.75612,0.146905,1.15727,0.218784,0.206105,1.07049,0.84426,0.913168,0.477584,1.25579,0.86037,0.684313,0.272514,1.10535,0.0481066,0.794988,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,1.55741,0.661488,0.987239,0.776336,0.166235,1.58445,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.826087,0.8388,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,0.683502,0.29379,0.661335,0.307168
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,0.436508,1.43205,1.01854,0.584466,0.662701,0.269608,1.35335,0.262261,0.553339,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.127969,0.436569,0.6169,0.576478,1.00694,0.483957,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,0.316592,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,1.6253,1.01199,0.354447,0.468392,0.66382,0.542147,1.56014,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.75612,0.146905,1.15727,0.218784,0.206105,1.07049,0.84426,0.913168,0.477584,1.25579,0.86037,0.684313,0.272514,1.10535,0.0481066,0.794988,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,1.55741,0.661488,0.987239,0.776336,0.166235,1.58445,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.826087,0.8388,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,0.683502,0.29379,0.661335,0.307168
|tfbs_overrepresentation_jaspar=MA0003.1;0.0799681,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.108006,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;1.34656,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.450439,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;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.0214749,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;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;1.02896,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.857383,MA0108.2;0.868347,MA0109.1;0,MA0111.1;1.25994,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;2.92176,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;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;1.95656,MA0143.1;0.725558,MA0144.1;0.811435,MA0145.1;0.707171,MA0146.1;0.093337,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.0313803,MA0138.2;1.80506,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.718489,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;1.09123,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;0.273773,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.0607789,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: C1416_corpus_diencephalon_medulla_spinal_thalamus_caudate_occipital



Phase1 CAGE Peaks

Hg19::chr15:93827399..93827403,+p@chr15:93827399..93827403
+
Hg19::chr16:70759540..70759547,+p@chr16:70759540..70759547
+
Hg19::chr17:73689469..73689476,-p@chr17:73689469..73689476
-
Hg19::chr1:234659231..234659238,-p@chr1:234659231..234659238
-
Hg19::chr5:7654271..7654280,+p14@ADCY2
Hg19::chr6:39335288..39335291,+p@chr6:39335288..39335291
+


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 tube2.54e-8456
neural rod2.54e-8456
future spinal cord2.54e-8456
neural keel2.54e-8456
regional part of nervous system2.26e-7653
regional part of brain2.26e-7653
regional part of forebrain6.28e-6441
forebrain6.28e-6441
anterior neural tube6.28e-6441
future forebrain6.28e-6441
telencephalon8.67e-6334
brain1.19e-6268
future brain1.19e-6268
brain grey matter3.09e-6234
gray matter3.09e-6234
central nervous system8.60e-6181
neural plate2.04e-5682
presumptive neural plate2.04e-5682
nervous system2.27e-5489
neurectoderm1.33e-5386
cerebral hemisphere5.66e-5332
regional part of telencephalon7.14e-5332
adult organism2.75e-46114
regional part of cerebral cortex1.14e-4422
ecto-epithelium1.39e-43104
pre-chordal neural plate5.49e-4261
neocortex1.11e-4120
cerebral cortex3.11e-3925
pallium3.11e-3925
structure with developmental contribution from neural crest3.91e-36132
brainstem6.55e-276
ectoderm-derived structure2.06e-26171
ectoderm2.06e-26171
presumptive ectoderm2.06e-26171
neural nucleus3.82e-259
nucleus of brain3.82e-259
tube1.89e-21192
organ system subdivision9.78e-21223
posterior neural tube1.82e-2015
chordal neural plate1.82e-2015
pons2.21e-193
basal ganglion5.17e-189
nuclear complex of neuraxis5.17e-189
aggregate regional part of brain5.17e-189
collection of basal ganglia5.17e-189
cerebral subcortex5.17e-189
gyrus3.88e-176
anatomical conduit3.64e-16240
telencephalic nucleus4.39e-157
temporal lobe9.77e-156
locus ceruleus1.75e-132
brainstem nucleus1.75e-132
hindbrain nucleus1.75e-132
segmental subdivision of hindbrain2.18e-1312
hindbrain2.18e-1312
presumptive hindbrain2.18e-1312
middle temporal gyrus2.92e-132
limbic system1.45e-125
segmental subdivision of nervous system2.41e-1213
occipital lobe2.41e-125
parietal lobe2.93e-125
epithelium1.40e-11306
cell layer2.04e-11309
organ part4.31e-11218
anatomical cluster2.17e-10373
medulla oblongata4.02e-103
myelencephalon4.02e-103
future myelencephalon4.02e-103
spinal cord9.30e-103
dorsal region element9.30e-103
dorsum9.30e-103
multi-tissue structure8.67e-09342
corpus callosum2.70e-081
central nervous system cell part cluster2.70e-081
axon tract2.70e-081
intercerebral commissure2.70e-081
dorsal telencephalic commissure2.70e-081
brain white matter2.70e-081
brain commissure2.70e-081
white matter2.70e-081
nervous system commissure2.70e-081
cerebral hemisphere white matter2.70e-081
nucleus accumbens5.70e-081
ventral striatum5.70e-081
olfactory region6.10e-081
primary subdivision of skull6.10e-081
cranium6.10e-081
neurocranium6.10e-081
chondrocranium6.10e-081
cartilaginous neurocranium6.10e-081
head paraxial mesoderm6.10e-081
paracentral gyrus6.52e-081
postcentral gyrus6.97e-081
occipital pole7.45e-081
pole of cerebral hemisphere7.45e-081
insula7.97e-081
substantia nigra1.04e-071
midbrain nucleus1.04e-071
regional part of midbrain1.04e-071
midbrain1.04e-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)
MA0003.10.0799681
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
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
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
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
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.12.92176
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.11.95656
MA0143.10.725558
MA0144.10.811435
MA0145.10.707171
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0313803
MA0138.21.80506
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.11.09123
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.0607789
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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