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Coexpression cluster:C1307: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,1.01544,0.415981,0.889639,0.336106,0.236034,0.127969,1.11315,0.0880431,0.576478,1.00694,0.483957,0.730467,0.585619,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.0334022,0.35388,0.585658,0.329602,0.248856,0.936389,0.513952,0.0979105,0.390088,0.154075,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,1.03549,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.75612,0.146905,1.15727,0.218784,0.206105,0.562953,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,1.37357,1.10535,0.0481066,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,1.10061,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,1.57878,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,1.94435,0.683502,0.29379,0.661335,0.0115686
|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;0.152639,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;0.267412,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;0.0214749,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;1.80244,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;1.37996,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;0.323925,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;0.107156,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;1.50688,MA0039.2;0.00570825,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;0.0270301,MA0164.1;1.74929,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;7.22997e-05,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: C1307_thalamus_globus_substantia_optic_spinal_locus_occipital



Phase1 CAGE Peaks

Hg19::chr10:22859761..22859773,-p@chr10:22859761..22859773
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Hg19::chr10:22871815..22871821,-p@chr10:22871815..22871821
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Hg19::chr10:22916514..22916517,-p@chr10:22916514..22916517
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Hg19::chr10:22963342..22963345,-p@chr10:22963342..22963345
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Hg19::chr10:22994352..22994355,-p@chr10:22994352..22994355
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Hg19::chr10:22998989..22998993,-p@chr10:22998989..22998993
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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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell6.08e-31168
angioblastic mesenchymal cell6.08e-31168
hematopoietic oligopotent progenitor cell1.47e-29161
hematopoietic multipotent progenitor cell1.47e-29161
hematopoietic cell1.47e-27177
leukocyte1.03e-24136
hematopoietic lineage restricted progenitor cell2.38e-23120
nongranular leukocyte4.78e-23115
nucleate cell2.05e-1555
myeloid cell5.45e-15108
common myeloid progenitor5.45e-15108
lymphocyte1.46e-1453
common lymphoid progenitor1.46e-1453
lymphoid lineage restricted progenitor cell1.55e-1452
myeloid lineage restricted progenitor cell1.12e-0966
mature alpha-beta T cell3.54e-0918
alpha-beta T cell3.54e-0918
immature T cell3.54e-0918
mature T cell3.54e-0918
immature alpha-beta T cell3.54e-0918
myeloid leukocyte4.04e-0972
classical monocyte5.83e-0942
CD14-positive, CD16-negative classical monocyte5.83e-0942
granulocyte monocyte progenitor cell8.94e-0967
T cell1.13e-0825
pro-T cell1.13e-0825
macrophage dendritic cell progenitor2.15e-0861
monopoietic cell2.61e-0859
monocyte2.61e-0859
monoblast2.61e-0859
promonocyte2.61e-0859
defensive cell1.13e-0748
phagocyte1.13e-0748
Uber Anatomy
Ontology termp-valuen
adult organism3.91e-28114
neural tube5.90e-2056
neural rod5.90e-2056
future spinal cord5.90e-2056
neural keel5.90e-2056
regional part of forebrain2.28e-1841
forebrain2.28e-1841
anterior neural tube2.28e-1841
future forebrain2.28e-1841
regional part of nervous system3.23e-1853
regional part of brain3.23e-1853
brain grey matter3.56e-1734
gray matter3.56e-1734
telencephalon6.47e-1734
brain3.11e-1668
future brain3.11e-1668
regional part of telencephalon7.36e-1632
central nervous system8.42e-1681
cerebral hemisphere1.25e-1532
nervous system7.86e-1589
hematopoietic system6.90e-1298
blood island6.90e-1298
cerebral cortex8.25e-1225
pallium8.25e-1225
hemolymphoid system1.89e-11108
regional part of cerebral cortex2.17e-1122
neurectoderm1.39e-1086
neural plate1.99e-1082
presumptive neural plate1.99e-1082
neocortex3.77e-1020
pre-chordal neural plate1.99e-0861
immune system7.65e-0893
neural nucleus5.40e-079
nucleus of brain5.40e-079
basal ganglion6.85e-079
nuclear complex of neuraxis6.85e-079
aggregate regional part of brain6.85e-079
collection of basal ganglia6.85e-079
cerebral subcortex6.85e-079
Disease
Ontology termp-valuen
hematologic cancer1.94e-0751
immune system cancer1.94e-0751


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
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
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
MA0073.10.0214749
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.11.80244
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.11.37996
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
MA0116.10.323925
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
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.21.50688
MA0039.20.00570825
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
MA0163.10.0270301
MA0164.11.74929
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.27.22997e-05
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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