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Coexpression cluster:C1543: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.223349,0.650887,0.391663,1.06849,0.889639,0.336106,0.236034,0.127969,1.11315,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.577216,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,1.10319,0.390088,0.354447,0.468392,0.66382,0.542147,0.630853,0.396429,0.745008,2.73134,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,1.50144,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.45007,1.15727,0.218784,1.12235,0.562953,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.864356,1.23175,0.987239,0.776336,0.166235,0.881389,0.938327,0.981588,0.893363,0.814675,1.35291,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,1.10061,0.563054,1.29401,0.928633,0.210279,0.529546,0.824029,0.840396,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,5.60657,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,1.48535,0.799467,2.01411,0.510514,0.826087,0.136746,1.06652,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,3.22613,0.683502,0.29379,0.661335,0.0564726
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.223349,0.650887,0.391663,1.06849,0.889639,0.336106,0.236034,0.127969,1.11315,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.577216,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,1.10319,0.390088,0.354447,0.468392,0.66382,0.542147,0.630853,0.396429,0.745008,2.73134,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,1.50144,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.45007,1.15727,0.218784,1.12235,0.562953,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.864356,1.23175,0.987239,0.776336,0.166235,0.881389,0.938327,0.981588,0.893363,0.814675,1.35291,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,1.10061,0.563054,1.29401,0.928633,0.210279,0.529546,0.824029,0.840396,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,5.60657,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,1.48535,0.799467,2.01411,0.510514,0.826087,0.136746,1.06652,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,3.22613,0.683502,0.29379,0.661335,0.0564726
|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;0.262822,MA0017.1;1.10421,MA0019.1;2.84728,MA0024.1;2.14259,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;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;0.457555,MA0060.1;0.737586,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;2.43863,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.216116,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;1.22966,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;0.134725,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;0.865577,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;1.86787,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;1.95656,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;0.621793,MA0039.2;1.13151,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;0.354331,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;0.65596,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;0.113377,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.35176,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: C1543_neuroectodermal_thalamus_temporal_diencephalon_occipital_substantia_duodenum



Phase1 CAGE Peaks

Hg19::chr8:26435519..26435548,+p3@DPYSL2
Hg19::chr8:26435581..26435592,+p9@DPYSL2
Hg19::chr8:26505189..26505239,+p@chr8:26505189..26505239
+
Hg19::chr8:26509826..26509911,+p@chr8:26509826..26509911
+
Hg19::chr8:26513317..26513334,+p2@DPYSL2
Hg19::chr8:26513702..26513722,+p4@DPYSL2


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
fibroblast2.72e-1076
electrically responsive cell2.69e-0861
electrically active cell2.69e-0861
non-terminally differentiated cell8.46e-07106
Uber Anatomy
Ontology termp-valuen
central nervous system1.60e-3081
nervous system2.35e-3089
neural tube7.55e-2756
neural rod7.55e-2756
future spinal cord7.55e-2756
neural keel7.55e-2756
brain2.61e-2568
future brain2.61e-2568
regional part of nervous system5.13e-2553
regional part of brain5.13e-2553
neurectoderm9.86e-2586
neural plate2.89e-2382
presumptive neural plate2.89e-2382
ectoderm-derived structure1.19e-20171
ectoderm1.19e-20171
presumptive ectoderm1.19e-20171
brain grey matter1.24e-2034
gray matter1.24e-2034
telencephalon1.43e-2034
regional part of forebrain3.83e-2041
forebrain3.83e-2041
anterior neural tube3.83e-2041
future forebrain3.83e-2041
structure with developmental contribution from neural crest4.04e-20132
regional part of telencephalon2.20e-1932
cerebral hemisphere2.86e-1932
multi-cellular organism9.88e-19656
tube1.61e-16192
anatomical cluster1.91e-16373
ecto-epithelium8.38e-16104
pre-chordal neural plate1.09e-1561
cerebral cortex2.70e-1525
pallium2.70e-1525
germ layer4.76e-15560
germ layer / neural crest4.76e-15560
embryonic tissue4.76e-15560
presumptive structure4.76e-15560
germ layer / neural crest derived structure4.76e-15560
epiblast (generic)4.76e-15560
anatomical system4.78e-15624
anatomical conduit8.29e-15240
anatomical group8.36e-15625
regional part of cerebral cortex1.51e-1422
embryonic structure2.79e-14564
cell layer5.32e-14309
epithelium1.02e-13306
neocortex2.72e-1320
organ system subdivision3.67e-13223
developing anatomical structure1.79e-12581
embryo1.15e-11592
adult organism1.94e-10114
multi-tissue structure2.16e-10342
organ part2.04e-09218
organ3.65e-09503
tissue1.25e-08773
posterior neural tube7.17e-0815
chordal neural plate7.17e-0815
neural nucleus8.32e-079
nucleus of brain8.32e-079
segmental subdivision of nervous system8.74e-0713
basal ganglion8.99e-079
nuclear complex of neuraxis8.99e-079
aggregate regional part of brain8.99e-079
collection of basal ganglia8.99e-079
cerebral subcortex8.99e-079


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
MA0014.10.262822
MA0017.11.10421
MA0019.12.84728
MA0024.12.14259
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
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.737586
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.12.43863
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.216116
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
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
MA0116.10.865577
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
MA0139.11.86787
MA0140.10.622527
MA0141.10.455728
MA0142.11.95656
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.21.13151
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.35176
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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