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Coexpression cluster:C1331: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.736703,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.402028,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,0.134746,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,1.6253,0.390088,0.354447,0.468392,0.66382,0.542147,1.56014,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.181326,4.85059,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,1.23175,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,1.10061,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.8388,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,14.8877,28.2843,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.521461
|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;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;1.3446,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;0.0586456,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;1.15845,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;15.3582,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;0.660742,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;0.397846,MA0103.1;0.993014,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.857383,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;0.865577,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;0.672893,MA0139.1;0.226048,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;0.0313803,MA0138.2;0.765223,MA0002.2;0.709311,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;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;0.273773,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.0146751,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:51, 22 January 2013


Full id: C1331_cerebellum_pineal_Neural_medulla_parietal_hippocampus_optic



Phase1 CAGE Peaks

Hg19::chr11:115263782..115263785,-p@chr11:115263782..115263785
-
Hg19::chr13:113685172..113685179,+p@chr13:113685172..113685179
+
Hg19::chr1:160163170..160163181,+p@chr1:160163170..160163181
+
Hg19::chr1:202594169..202594182,-p@chr1:202594169..202594182
-
Hg19::chr20:62864254..62864290,+p@chr20:62864254..62864290
+
Hg19::chr6:37615324..37615328,-p21@MDGA1


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
regional part of nervous system4.07e-8553
regional part of brain4.07e-8553
neural tube1.80e-8056
neural rod1.80e-8056
future spinal cord1.80e-8056
neural keel1.80e-8056
brain6.24e-6568
future brain6.24e-6568
central nervous system2.98e-5481
neural plate2.98e-5482
presumptive neural plate2.98e-5482
regional part of forebrain4.21e-5441
forebrain4.21e-5441
anterior neural tube4.21e-5441
future forebrain4.21e-5441
neurectoderm1.32e-5186
brain grey matter1.19e-5034
gray matter1.19e-5034
nervous system1.27e-4889
cerebral hemisphere1.65e-4632
telencephalon1.01e-4334
ecto-epithelium3.41e-42104
regional part of telencephalon4.19e-4032
pre-chordal neural plate9.59e-3661
adult organism3.45e-35114
brainstem1.62e-346
regional part of cerebral cortex2.44e-3422
segmental subdivision of hindbrain1.77e-3312
hindbrain1.77e-3312
presumptive hindbrain1.77e-3312
structure with developmental contribution from neural crest1.33e-32132
segmental subdivision of nervous system7.46e-3113
neocortex2.01e-3020
cerebral cortex3.29e-3025
pallium3.29e-3025
posterior neural tube1.18e-2615
chordal neural plate1.18e-2615
pons1.46e-253
ectoderm-derived structure4.14e-24171
ectoderm4.14e-24171
presumptive ectoderm4.14e-24171
regional part of metencephalon2.72e-239
metencephalon2.72e-239
future metencephalon2.72e-239
neural nucleus2.98e-239
nucleus of brain2.98e-239
tube2.16e-21192
regional part of diencephalon6.89e-204
pineal body1.89e-182
regional part of epithalamus1.89e-182
secretory circumventricular organ1.89e-182
circumventricular organ1.89e-182
epithalamus1.89e-182
locus ceruleus5.75e-182
brainstem nucleus5.75e-182
hindbrain nucleus5.75e-182
organ system subdivision1.18e-17223
anatomical conduit2.01e-16240
limbic system1.35e-155
basal ganglion4.79e-159
nuclear complex of neuraxis4.79e-159
aggregate regional part of brain4.79e-159
collection of basal ganglia4.79e-159
cerebral subcortex4.79e-159
organ part2.57e-13218
gyrus5.30e-136
epithelium4.16e-12306
medulla oblongata4.22e-123
myelencephalon4.22e-123
future myelencephalon4.22e-123
frontal cortex4.99e-123
cell layer5.91e-12309
diencephalon1.31e-117
future diencephalon1.31e-117
telencephalic nucleus2.32e-117
temporal lobe3.42e-116
multi-tissue structure2.10e-10342
gland of diencephalon1.10e-094
neuroendocrine gland1.10e-094
nucleus accumbens1.62e-091
ventral striatum1.62e-091
insula1.91e-091
paracentral gyrus2.46e-091
corpus striatum3.44e-094
striatum3.44e-094
ventral part of telencephalon3.44e-094
future corpus striatum3.44e-094
anatomical cluster3.66e-09373
parietal lobe1.61e-075


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
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.11.3446
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.11.15845
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
MA0073.115.3582
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.10.134725
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
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
MA0136.10.672893
MA0139.10.226048
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
MA0039.20.0313803
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
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
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.0146751
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ZNF274#107821236.9576923076920.004212805738819990.02005475265767



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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