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Coexpression cluster:C1328: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,1.01854,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.223349,0.650887,1.01544,1.06849,0.889639,0.336106,0.236034,1.30166,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,1.19786,0.35719,0.316592,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,0.0393783,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,1.57403,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,2.00306,0.684675,0.826413,1.24834,1.61834,2.11566,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,2.31006,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,1.9262,0.312699,1.14892,0.769145,3.55449,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,1.27188,2.2813,0.424432,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,1.63571,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,1.01854,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.223349,0.650887,1.01544,1.06849,0.889639,0.336106,0.236034,1.30166,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,1.19786,0.35719,0.316592,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,0.0393783,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,1.57403,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,2.00306,0.684675,0.826413,1.24834,1.61834,2.11566,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,2.31006,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,1.9262,0.312699,1.14892,0.769145,3.55449,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,1.27188,2.2813,0.424432,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,1.63571,0.29379,0.661335,0.0115686
|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;0.871496,MA0038.1;0.665566,MA0040.1;2.19519,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;0.0586456,MA0056.1;0,MA0057.1;0.450439,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.737586,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;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;0.32124,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;0.381434,MA0105.1;0.419295,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;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;1.72302,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;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;4.16572,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;0.508943,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: C1328_extraskeletal_cerebellum_brain_duodenum_occipital_parietal_temporal



Phase1 CAGE Peaks

Hg19::chr11:105480958..105480979,+p7@GRIA4
Hg19::chr21:17442864..17442881,+p11@LINC00478
Hg19::chr21:17442981..17443002,+p7@LINC00478
Hg19::chr5:140743720..140743735,+p3@PCDHGA5
Hg19::chr5:140743737..140743773,+p1@PCDHGA5
Hg19::chr5:140743798..140743812,+p5@PCDHGA5


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:0007215glutamate signaling pathway0.0359506809929164
GO:0004970ionotropic glutamate receptor activity0.0359506809929164
GO:0005234extracellular-glutamate-gated ion channel activity0.0359506809929164
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0452696791342411
GO:0008066glutamate receptor activity0.0452696791342411
GO:0005230extracellular ligand-gated ion channel activity0.0452696791342411
GO:0045211postsynaptic membrane0.0452696791342411
GO:0044456synapse part0.0452696791342411
GO:0015276ligand-gated ion channel activity0.0452696791342411
GO:0022834ligand-gated channel activity0.0452696791342411
GO:0007156homophilic cell adhesion0.0494071807938995
GO:0005886plasma membrane0.0494071807938995



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 tube2.61e-6056
neural rod2.61e-6056
future spinal cord2.61e-6056
neural keel2.61e-6056
regional part of nervous system7.82e-5753
regional part of brain7.82e-5753
central nervous system7.97e-5381
neural plate1.69e-4982
presumptive neural plate1.69e-4982
neurectoderm2.73e-4986
nervous system2.69e-4889
adult organism8.30e-45114
brain1.17e-4468
future brain1.17e-4468
regional part of forebrain1.44e-4341
forebrain1.44e-4341
anterior neural tube1.44e-4341
future forebrain1.44e-4341
telencephalon3.20e-3634
brain grey matter4.49e-3634
gray matter4.49e-3634
ecto-epithelium2.21e-35104
pre-chordal neural plate2.36e-3461
cerebral hemisphere3.51e-3432
regional part of telencephalon5.97e-3432
structure with developmental contribution from neural crest1.87e-31132
cerebral cortex1.73e-2625
pallium1.73e-2625
ectoderm-derived structure2.22e-26171
ectoderm2.22e-26171
presumptive ectoderm2.22e-26171
regional part of cerebral cortex2.99e-2422
organ system subdivision8.90e-23223
neocortex2.73e-2220
posterior neural tube3.22e-1715
chordal neural plate3.22e-1715
segmental subdivision of hindbrain5.13e-1412
hindbrain5.13e-1412
presumptive hindbrain5.13e-1412
anatomical cluster1.64e-13373
multi-tissue structure9.95e-13342
segmental subdivision of nervous system1.26e-1213
cell layer1.63e-11309
tube1.76e-11192
epithelium4.11e-11306
regional part of metencephalon4.61e-119
metencephalon4.61e-119
future metencephalon4.61e-119
neural nucleus6.13e-119
nucleus of brain6.13e-119
basal ganglion8.51e-119
nuclear complex of neuraxis8.51e-119
aggregate regional part of brain8.51e-119
collection of basal ganglia8.51e-119
cerebral subcortex8.51e-119
anatomical conduit1.06e-10240
multi-cellular organism3.33e-10656
organ4.86e-10503
organ part2.57e-09218
telencephalic nucleus6.79e-097
anatomical system6.93e-09624
anatomical group8.38e-09625
diencephalon1.25e-087
future diencephalon1.25e-087
gyrus2.97e-086
cerebellum6.23e-086
rhombic lip6.23e-086
brainstem1.03e-076
tissue1.07e-07773
occipital lobe3.30e-075
parietal lobe4.17e-075
temporal lobe9.91e-076


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
MA0031.10.871496
MA0038.10.665566
MA0040.12.19519
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.737586
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
MA0074.11.58758
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
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
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.11.72302
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
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.14.16572
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
MA0163.10.508943
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
CTCF#1066465.360256373075034.21437267579784e-050.000754965468074872



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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