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Coexpression cluster:C1305: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,1.30166,0.436569,0.0880431,0.576478,0.387783,1.21515,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,2.82399,0.35388,0.585658,0.878269,0.248856,0.936389,0.513952,1.10319,2.68609,0.354447,1.18176,0.66382,0.542147,1.05432,0.396429,0.745008,0.675919,0.455399,1.00488,4.23287,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,1.25018,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,1.63739,0.272514,1.10535,0.181326,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.864356,0.234532,2.26006,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,1.57878,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,1.65434,1.35529,0.175219,4.45611,1.40818,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,1.78411,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0564726
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,1.30166,0.436569,0.0880431,0.576478,0.387783,1.21515,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,2.82399,0.35388,0.585658,0.878269,0.248856,0.936389,0.513952,1.10319,2.68609,0.354447,1.18176,0.66382,0.542147,1.05432,0.396429,0.745008,0.675919,0.455399,1.00488,4.23287,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,1.25018,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,1.63739,0.272514,1.10535,0.181326,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.864356,0.234532,2.26006,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,1.57878,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,1.65434,1.35529,0.175219,4.45611,1.40818,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,1.78411,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0564726
|tfbs_overrepresentation_jaspar=MA0003.1;0.00461978,MA0004.1;3.45359,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;0.147053,MA0058.1;2.02413,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;0.347876,MA0074.1;1.58758,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;3.70023,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;1.52717,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;1.84113,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;1.86787,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;1.47313,MA0145.1;0.107156,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;2.43826,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;1.87543,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;1.7308,MA0150.1;0.484557,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;3.63746,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 19:50, 22 January 2013


Full id: C1305_neuroectodermal_medulla_retina_peripheral_hippocampus_caudate_pituitary



Phase1 CAGE Peaks

Hg19::chr10:18240899..18240911,+p3@SLC39A12
Hg19::chr12:20848282..20848305,+p6@SLCO1C1
Hg19::chr12:20848316..20848349,+p3@SLCO1C1
Hg19::chr12:20848377..20848399,+p5@SLCO1C1
Hg19::chr12:20848404..20848452,+p2@SLCO1C1
Hg19::chr12:20848471..20848483,+p8@SLCO1C1


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:0006829zinc ion transport0.0185258703232524
GO:0006811ion transport0.0185258703232524
GO:0000041transition metal ion transport0.0459694753598906



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
neuronal stem cell5.18e-098
Uber Anatomy
Ontology termp-valuen
neural tube8.98e-9856
neural rod8.98e-9856
future spinal cord8.98e-9856
neural keel8.98e-9856
central nervous system3.50e-9581
regional part of nervous system2.16e-9153
regional part of brain2.16e-9153
nervous system5.15e-8789
regional part of forebrain1.23e-8241
forebrain1.23e-8241
anterior neural tube1.23e-8241
future forebrain1.23e-8241
brain1.56e-7668
future brain1.56e-7668
neurectoderm5.26e-7086
telencephalon1.58e-6834
brain grey matter3.05e-6834
gray matter3.05e-6834
neural plate7.99e-6882
presumptive neural plate7.99e-6882
regional part of telencephalon3.13e-6432
cerebral hemisphere4.54e-6432
adult organism2.34e-61114
pre-chordal neural plate6.00e-5561
ecto-epithelium2.87e-50104
cerebral cortex3.42e-4925
pallium3.42e-4925
structure with developmental contribution from neural crest1.00e-46132
ectoderm-derived structure6.56e-46171
ectoderm6.56e-46171
presumptive ectoderm6.56e-46171
regional part of cerebral cortex3.12e-4422
neocortex1.01e-3920
organ system subdivision1.09e-32223
tube3.14e-23192
basal ganglion1.44e-209
nuclear complex of neuraxis1.44e-209
aggregate regional part of brain1.44e-209
collection of basal ganglia1.44e-209
cerebral subcortex1.44e-209
neural nucleus4.56e-209
nucleus of brain4.56e-209
anatomical cluster9.33e-20373
anatomical conduit5.10e-18240
posterior neural tube1.35e-1615
chordal neural plate1.35e-1615
telencephalic nucleus2.99e-167
diencephalon5.31e-157
future diencephalon5.31e-157
gyrus3.30e-146
brainstem3.62e-146
limbic system1.72e-125
epithelium3.11e-12306
cell layer5.77e-12309
temporal lobe1.07e-116
occipital lobe1.32e-115
parietal lobe1.64e-115
segmental subdivision of hindbrain2.78e-1112
hindbrain2.78e-1112
presumptive hindbrain2.78e-1112
multi-tissue structure7.19e-11342
segmental subdivision of nervous system2.73e-1013
corpus striatum7.38e-104
striatum7.38e-104
ventral part of telencephalon7.38e-104
future corpus striatum7.38e-104
organ part1.25e-09218
regional part of diencephalon2.06e-094
gland of diencephalon6.08e-094
neuroendocrine gland6.08e-094
medulla oblongata1.94e-083
myelencephalon1.94e-083
future myelencephalon1.94e-083
frontal cortex6.11e-083
caudate-putamen7.86e-083
dorsal striatum7.86e-083
embryo8.06e-08592
spinal cord1.41e-073
dorsal region element1.41e-073
dorsum1.41e-073
pons2.02e-073
germ layer2.40e-07560
germ layer / neural crest2.40e-07560
embryonic tissue2.40e-07560
presumptive structure2.40e-07560
germ layer / neural crest derived structure2.40e-07560
epiblast (generic)2.40e-07560
developing anatomical structure2.68e-07581
embryonic structure3.69e-07564


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)
MA0003.10.00461978
MA0004.13.45359
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
MA0057.10.147053
MA0058.12.02413
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
MA0073.10.347876
MA0074.11.58758
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
MA0093.13.70023
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
MA0114.11.52717
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.86787
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.11.47313
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.12.43826
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.21.87543
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.21.7308
MA0150.10.484557
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
MA0160.13.63746
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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