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Coexpression cluster:C2436: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,2.42852,0.741427,0.534346,0.739643,0.821651,1.81026,1.01802,0.902371,0.706765,0.867962,0.341754,1.89595,0.532789,0.559384,1.05593,0.471262,1.67497,1.18986,0.581762,1.55218,0.731221,0.528529,0.632849,0.892087,4.19021,2.89941,0.537869,0.297585,1.63433,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.971732,0.493145,1.59701,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,2.09659,0.83543,0.699149,1.17354,1.33024,1.90242,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,1.28263,1.32819,1.6033,1.54953,0.305238,1.00941,5.65546,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,0.716653,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.749003,0.465545,1.1057,1.14983,1.05974,3.67962,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.785429,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,1.58968,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,2.42852,0.741427,0.534346,0.739643,0.821651,1.81026,1.01802,0.902371,0.706765,0.867962,0.341754,1.89595,0.532789,0.559384,1.05593,0.471262,1.67497,1.18986,0.581762,1.55218,0.731221,0.528529,0.632849,0.892087,4.19021,2.89941,0.537869,0.297585,1.63433,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.971732,0.493145,1.59701,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,2.09659,0.83543,0.699149,1.17354,1.33024,1.90242,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,1.28263,1.32819,1.6033,1.54953,0.305238,1.00941,5.65546,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,0.716653,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.749003,0.465545,1.1057,1.14983,1.05974,3.67962,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.785429,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,1.58968,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_jaspar=MA0003.1;9.1772,MA0004.1;2.8475,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.244769,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;0.396851,MA0056.1;0,MA0057.1;0.248209,MA0058.1;1.47358,MA0059.1;1.47051,MA0060.1;2.70115,MA0061.1;0.360128,MA0063.1;0,MA0066.1;7.65991,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;1.17185,MA0088.1;1.62583,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;3.35176,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;1.29536,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;6.43968,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;2.17614,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;10.27,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;2.2938,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;1.25938,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;1.66396,MA0035.2;0.778873,MA0039.2;2.01147,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;2.35508,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;6.35649,MA0155.1;1.02191,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;1.78721,MA0161.1;0,MA0162.1;0.309472,MA0163.1;1.90765,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;2.00408,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;6.55566,MA0442.1;0
}}
}}

Revision as of 20:40, 22 January 2013


Full id: C2436_serous_gastric_argyrophil_gall_smallcell_gastrointestinal_acantholytic



Phase1 CAGE Peaks

Hg19::chr17:74136040..74136061,-p2@AB463648
p2@AB464532
Hg19::chr17:74136069..74136082,-p3@AB463648
p3@AB464532
Hg19::chr17:74136083..74136116,-p1@AB463648
p1@AB464532
Hg19::chr17:74136122..74136132,-p4@AB463648
p4@AB464532


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>

Uber Anatomy
Ontology termp-valuen
male reproductive organ4.17e-1611
testis1.51e-138
cavitated compound organ3.43e-1131
male organism1.98e-1022
male reproductive system1.98e-1022
kidney3.18e-1026
kidney mesenchyme3.18e-1026
upper urinary tract3.18e-1026
kidney rudiment3.18e-1026
kidney field3.18e-1026
excretory tube6.60e-1016
kidney epithelium6.60e-1016
reproductive organ1.35e-0948
reproductive structure4.99e-0959
reproductive system4.99e-0959
anatomical space6.55e-0995
male genital duct1.84e-083
internal male genitalia1.84e-083
duct1.89e-0819
nephron epithelium2.59e-0815
renal tubule2.59e-0815
nephron tubule2.59e-0815
nephron2.59e-0815
uriniferous tubule2.59e-0815
nephrogenic mesenchyme2.59e-0815
urinary system structure2.91e-0847
cortex of kidney3.76e-0812
renal parenchyma3.76e-0812
adult organism4.30e-08114
renal system5.19e-0848
immaterial anatomical entity1.46e-07117
nephron tubule epithelium1.55e-0710
gonad2.54e-0721
indifferent external genitalia2.54e-0721
indifferent gonad2.54e-0721
gonad primordium2.54e-0721
trunk region element3.16e-07101
medulla oblongata3.18e-073
myelencephalon3.18e-073
future myelencephalon3.18e-073
external genitalia6.59e-0722
body cavity precursor6.63e-0754
Disease
Ontology termp-valuen
carcinoma1.10e-08106
cell type cancer3.15e-07143


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)
MA0003.19.1772
MA0004.12.8475
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
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
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.11.47051
MA0060.12.70115
MA0061.10.360128
MA0063.10
MA0066.17.65991
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
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.13.35176
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
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
MA0116.16.43968
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.110.27
MA0140.10.779643
MA0141.10.602484
MA0142.12.2938
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.22.35508
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.16.35649
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.10.309472
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.00408
MA0102.21.75932
MA0258.10.418966
MA0259.16.55566
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#1066445.360256373075030.001211145381643620.00817176901049669
SUZ12#23512450.11578091106291.5827390373096e-078.80190001691043e-06



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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