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Coexpression cluster:C1546: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,3.57439,0.393082,0.584466,0.662701,0.742622,0.267027,0.075749,0.553339,1.68496,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.127969,0.436569,0.0880431,0.576478,1.00694,0.483957,0.730467,0.585619,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.0334022,0.35388,0.585658,0.329602,1.28576,0.355745,0.513952,0.323162,1.79057,0.0393783,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,1.61993,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,1.20149,1.25579,0.86037,1.63739,0.749276,1.10535,0.0481066,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,1.5087,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.840396,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,2.3703,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,1.48535,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,3.57439,0.393082,0.584466,0.662701,0.742622,0.267027,0.075749,0.553339,1.68496,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.127969,0.436569,0.0880431,0.576478,1.00694,0.483957,0.730467,0.585619,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.0334022,0.35388,0.585658,0.329602,1.28576,0.355745,0.513952,0.323162,1.79057,0.0393783,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,1.61993,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,1.20149,1.25579,0.86037,1.63739,0.749276,1.10535,0.0481066,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,1.5087,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.840396,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,2.3703,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,1.48535,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_jaspar=MA0003.1;0.00461978,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;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.464411,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;0.267412,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;2.30704,MA0071.1;3.74531,MA0072.1;2.29768,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;0.561458,MA0092.1;2.2336,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;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;0.347815,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;0.101413,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;0.0270301,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;1.69036,MA0099.2;0.629739,MA0079.2;5.9246e-06,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 20:00, 22 January 2013


Full id: C1546_medial_parietal_occipital_Adipocyte_Neurons_temporal_duodenum



Phase1 CAGE Peaks

Hg19::chr8:80567244..80567265,+p6@STMN2
Hg19::chr8:80577112..80577148,+p@chr8:80577112..80577148
+
Hg19::chr8:80577185..80577204,+p@chr8:80577185..80577204
+
Hg19::chr8:80577511..80577528,+p@chr8:80577511..80577528
+
Hg19::chr8:80577550..80577567,+p@chr8:80577550..80577567
+
Hg19::chr8:80577672..80577679,+p@chr8:80577672..80577679
+


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

Cell Type
Ontology termp-valuen
preadipocyte of the breast2.73e-073
Uber Anatomy
Ontology termp-valuen
neural tube6.75e-7056
neural rod6.75e-7056
future spinal cord6.75e-7056
neural keel6.75e-7056
regional part of nervous system3.15e-6753
regional part of brain3.15e-6753
central nervous system1.77e-6281
nervous system9.53e-6089
brain1.29e-5768
future brain1.29e-5768
regional part of forebrain3.24e-5341
forebrain3.24e-5341
anterior neural tube3.24e-5341
future forebrain3.24e-5341
brain grey matter4.79e-5134
gray matter4.79e-5134
cerebral hemisphere1.43e-5032
telencephalon1.75e-5034
regional part of cerebral cortex5.72e-4722
regional part of telencephalon6.79e-4732
neural plate6.37e-4482
presumptive neural plate6.37e-4482
neocortex1.67e-4220
neurectoderm2.60e-4186
cerebral cortex9.24e-4125
pallium9.24e-4125
ecto-epithelium1.46e-35104
pre-chordal neural plate7.81e-3361
adult organism6.31e-28114
ectoderm-derived structure4.16e-27171
ectoderm4.16e-27171
presumptive ectoderm4.16e-27171
structure with developmental contribution from neural crest1.90e-25132
organ system subdivision1.81e-22223
posterior neural tube4.51e-1715
chordal neural plate4.51e-1715
segmental subdivision of hindbrain1.23e-1412
hindbrain1.23e-1412
presumptive hindbrain1.23e-1412
gyrus1.91e-146
brainstem1.47e-136
segmental subdivision of nervous system2.31e-1313
tube7.49e-13192
temporal lobe1.16e-126
parietal lobe1.31e-125
occipital lobe2.49e-125
limbic system2.49e-125
basal ganglion6.43e-129
nuclear complex of neuraxis6.43e-129
aggregate regional part of brain6.43e-129
collection of basal ganglia6.43e-129
cerebral subcortex6.43e-129
neural nucleus1.12e-119
nucleus of brain1.12e-119
organ part4.04e-10218
corpus striatum1.66e-094
striatum1.66e-094
ventral part of telencephalon1.66e-094
future corpus striatum1.66e-094
regional part of metencephalon1.91e-099
metencephalon1.91e-099
future metencephalon1.91e-099
frontal cortex4.06e-083
anatomical conduit4.25e-08240
pons5.67e-083
telencephalic nucleus6.81e-087
caudate-putamen1.04e-073
dorsal striatum1.04e-073
anatomical cluster1.27e-07373
small intestine1.99e-074
medulla oblongata2.92e-073
myelencephalon2.92e-073
future myelencephalon2.92e-073
omentum7.65e-076
peritoneum7.65e-076
abdominal cavity7.65e-076
visceral peritoneum7.65e-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)
MA0003.10.00461978
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
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.12.30704
MA0071.13.74531
MA0072.12.29768
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
MA0091.10.561458
MA0092.12.2336
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
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
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
MA0112.20.101413
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
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.21.69036
MA0099.20.629739
MA0079.25.9246e-06
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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