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Coexpression cluster:C2165: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.44014,2.11192,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,2.39977,0.471262,5.58048,1.85448,0.581762,2.21632,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.806311,1.63433,1.09415,0.433165,0.344471,3.16804,0.285913,2.13139,0.740899,0.463978,0.971732,0.493145,0.66492,0.183156,0.53106,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,1.94963,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,5.3994,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,3.02769,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,2.16273,6.91071,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,4.4082,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,2.51097,0.681522,2.26288,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,3.0147,1.24902,1.76758,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.4289
|tfbs_overrepresentation_for_novel_motifs=1.44014,2.11192,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,2.39977,0.471262,5.58048,1.85448,0.581762,2.21632,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.806311,1.63433,1.09415,0.433165,0.344471,3.16804,0.285913,2.13139,0.740899,0.463978,0.971732,0.493145,0.66492,0.183156,0.53106,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,1.94963,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,5.3994,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,3.02769,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,2.16273,6.91071,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,4.4082,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,2.51097,0.681522,2.26288,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,3.0147,1.24902,1.76758,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.4289
|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;2.8475,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;4.49713,MA0017.1;0.577281,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;2.82503,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;2.526,MA0056.1;0,MA0057.1;0.248209,MA0058.1;1.47358,MA0059.1;4.90158,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;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,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;1.94315,MA0139.1;2.47057,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;5.03067,MA0145.1;0.569905,MA0146.1;2.92476,MA0147.1;5.25242,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;1.66396,MA0035.2;0.778873,MA0039.2;1.13403,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;2.35208,MA0104.2;4.75635,MA0047.2;0.856092,MA0112.2;0.187982,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;4.65937,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;3.3522,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;4.15404,MA0442.1;0
}}
}}

Revision as of 20:28, 22 January 2013


Full id: C2165_mesothelioma_adenocarcinoma_epidermoid_breast_colon_argyrophil_Prostate



Phase1 CAGE Peaks

Hg19::chr11:75140914..75140942,-p2@KLHL35
Hg19::chr11:75140966..75140979,-p7@KLHL35
Hg19::chr11:75140985..75141007,-p4@KLHL35
Hg19::chr11:75141017..75141039,-p3@KLHL35


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
germ line cell4.20e-077
germ cell4.20e-077
Uber Anatomy
Ontology termp-valuen
neural tube1.60e-2756
neural rod1.60e-2756
future spinal cord1.60e-2756
neural keel1.60e-2756
regional part of forebrain5.87e-2641
forebrain5.87e-2641
anterior neural tube5.87e-2641
future forebrain5.87e-2641
regional part of nervous system1.35e-2553
regional part of brain1.35e-2553
brain grey matter1.85e-2534
gray matter1.85e-2534
telencephalon3.67e-2534
cerebral hemisphere5.74e-2532
regional part of telencephalon1.39e-2232
regional part of cerebral cortex3.28e-2022
neocortex4.07e-2020
brain4.60e-1968
future brain4.60e-1968
central nervous system1.84e-1881
cerebral cortex2.58e-1725
pallium2.58e-1725
neural plate7.54e-1682
presumptive neural plate7.54e-1682
nervous system1.12e-1589
pre-chordal neural plate5.14e-1561
neurectoderm1.08e-1486
adult organism1.89e-12114
ecto-epithelium1.17e-11104
neural nucleus8.79e-109
nucleus of brain8.79e-109
parietal lobe1.09e-095
structure with developmental contribution from neural crest2.45e-09132
testis1.03e-088
corpus striatum1.81e-084
striatum1.81e-084
ventral part of telencephalon1.81e-084
future corpus striatum1.81e-084
gyrus4.52e-086
male reproductive organ6.07e-0811
organ system subdivision7.06e-08223
tube2.50e-07192
organ part3.08e-07218
basal ganglion3.60e-079
nuclear complex of neuraxis3.60e-079
aggregate regional part of brain3.60e-079
collection of basal ganglia3.60e-079
cerebral subcortex3.60e-079
caudate-putamen6.20e-073
dorsal striatum6.20e-073
pons8.33e-073
telencephalic nucleus8.61e-077
Disease
Ontology termp-valuen
cervical cancer4.05e-075


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)
MA0003.10.720743
MA0004.12.8475
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.14.49713
MA0017.10.577281
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
MA0048.12.82503
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.12.526
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.14.90158
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
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
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
MA0136.11.94315
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.15.03067
MA0145.10.569905
MA0146.12.92476
MA0147.15.25242
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.22.35208
MA0104.24.75635
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.14.65937
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.23.3522
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.14.15404
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#1066445.360256373075030.001211145381643620.00815964472413097
E2F6#187645.017155731697390.00157802193473060.00995271651919373
ELF1#199744.258097958807540.003041525565781240.0160593472479589
MAX#414946.452555509007120.0005767613195645490.00484604790458583
MYC#460945.22228187160940.001344309395272740.00885905659596727
NRF1#4899412.21027944771094.49717228915276e-050.00079204077016328
REST#597837.237521537096020.004104697304192610.0195704397056641
TCF7L2#6934410.77017656313737.42969445082454e-050.00115177357688832
USF1#739146.361499277207960.0006105011399140830.00507079120021369



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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