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Coexpression cluster:C2085: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,1.55218,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,2.46824,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.648765,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,1.98497,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,3.17561,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,1.55218,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,2.46824,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.648765,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,1.98497,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,3.17561,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;1.69588,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;2.4142,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;1.47358,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;2.63476,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;2.27878,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;1.46638,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.98779,MA0137.2;1.37305,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;1.78721,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;1.88931,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:23, 22 January 2013


Full id: C2085_Melanocyte_melanoma_retina_substantia_spinal_left_vagina



Phase1 CAGE Peaks

Hg19::chr10:97181989..97182006,-p8@SORBS1
Hg19::chr10:97182014..97182028,-p17@SORBS1
Hg19::chr10:97182043..97182098,-p5@SORBS1
Hg19::chr19:29374516..29374529,+p@chr19:29374516..29374529
+


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
melanocyte5.79e-1210
melanoblast5.79e-1210
pigment cell5.25e-0814
light melanocyte3.76e-073
Uber Anatomy
Ontology termp-valuen
adult organism9.26e-86114
neural tube8.29e-3456
neural rod8.29e-3456
future spinal cord8.29e-3456
neural keel8.29e-3456
regional part of nervous system2.27e-2953
regional part of brain2.27e-2953
neural plate3.66e-2782
presumptive neural plate3.66e-2782
neurectoderm2.66e-2586
central nervous system8.57e-2581
ecto-epithelium1.13e-22104
nervous system1.80e-2289
regional part of forebrain2.29e-2241
forebrain2.29e-2241
anterior neural tube2.29e-2241
future forebrain2.29e-2241
brain1.77e-2168
future brain1.77e-2168
structure with developmental contribution from neural crest4.93e-21132
brain grey matter1.59e-1734
gray matter1.59e-1734
telencephalon1.80e-1734
organ system subdivision1.87e-17223
ectoderm-derived structure9.05e-16171
ectoderm9.05e-16171
presumptive ectoderm9.05e-16171
regional part of telencephalon2.40e-1532
pre-chordal neural plate2.94e-1561
cerebral hemisphere6.07e-1532
posterior neural tube1.00e-1215
chordal neural plate1.00e-1215
anatomical cluster2.65e-11373
regional part of cerebral cortex3.27e-1122
neural nucleus6.03e-119
nucleus of brain6.03e-119
multi-tissue structure9.97e-11342
brainstem1.34e-106
anatomical conduit3.00e-10240
cerebral cortex1.66e-0925
pallium1.66e-0925
segmental subdivision of nervous system1.80e-0913
neocortex4.60e-0920
tube9.70e-09192
telencephalic nucleus2.18e-087
basal ganglion2.54e-089
nuclear complex of neuraxis2.54e-089
aggregate regional part of brain2.54e-089
collection of basal ganglia2.54e-089
cerebral subcortex2.54e-089
segmental subdivision of hindbrain3.20e-0812
hindbrain3.20e-0812
presumptive hindbrain3.20e-0812
regional part of diencephalon3.74e-084
organ9.51e-08503
spinal cord5.84e-073
dorsal region element5.84e-073
dorsum5.84e-073


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)
MA0003.10.0214529
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.12.4142
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.12.63476
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.98779
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.11.88931
MA0259.10.471671
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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