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Coexpression cluster:C2380: Difference between revisions

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{{Coexpression_clusters
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67,1.33003,0.297585,0.682839,1.09415,5.05028,0.911389,0.49475,2.05579,0.491074,1.75478,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,1.08066,0.61613,1.92371,1.65941,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,1.90242,0.54284,0.777235,1.46445,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,0.692875,1.32819,0.336329,1.54953,0.823598,1.00941,1.08,1.51572,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.749003,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,2.86199,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,2.92401,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,1.00204,1.24902,0.383416,0.824835,1.65997,2.11789,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,2.50192,0.997702,0.843324,4.98142,0.820225,0.359498|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.244769,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;2.02223,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.69331,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;1.68681,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;1.52107,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;1.18043,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;0.182167,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;8.55582,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;2.47057,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;4.04391,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.257871,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;2.43626,MA0150.1;3.7809,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.61785,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;4.43825,MA0079.2;2.72671,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2380_Melanocyte_mesothelioma_Renal_Neural_renal_Endothelial_Hepatic
|id=C2380
}}

Latest revision as of 12:04, 17 September 2013


Full id: C2380_Melanocyte_mesothelioma_Renal_Neural_renal_Endothelial_Hepatic



Phase1 CAGE Peaks

Hg19::chr16:57662515..57662526,+p8@GPR56
Hg19::chr16:57662527..57662556,+p1@GPR56
Hg19::chr16:57662566..57662582,+p6@GPR56
Hg19::chr16:57662596..57662613,+p2@GPR56


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>

Uber Anatomy
Ontology termp-valuen
adult organism1.26e-29114
neural plate3.98e-2282
presumptive neural plate3.98e-2282
neural tube3.61e-2156
neural rod3.61e-2156
future spinal cord3.61e-2156
neural keel3.61e-2156
central nervous system1.04e-1981
regional part of nervous system1.12e-1953
regional part of brain1.12e-1953
anatomical cluster3.46e-19373
tube5.82e-19192
anatomical conduit6.35e-19240
neurectoderm8.98e-1986
brain2.98e-1868
future brain2.98e-1868
structure with developmental contribution from neural crest4.02e-17132
ecto-epithelium2.15e-16104
nervous system7.18e-1689
pre-chordal neural plate7.25e-1661
regional part of forebrain1.38e-1541
forebrain1.38e-1541
anterior neural tube1.38e-1541
future forebrain1.38e-1541
cell layer2.77e-14309
epithelium6.97e-14306
brain grey matter1.85e-1334
gray matter1.85e-1334
telencephalon3.21e-1334
regional part of telencephalon2.24e-1232
cerebral hemisphere2.78e-1232
blood vessel endothelium4.16e-1118
endothelium4.16e-1118
cardiovascular system endothelium4.16e-1118
ectoderm-derived structure2.22e-10171
ectoderm2.22e-10171
presumptive ectoderm2.22e-10171
multi-tissue structure2.49e-09342
cerebral cortex7.32e-0925
pallium7.32e-0925
simple squamous epithelium2.70e-0822
anatomical system3.12e-08624
regional part of cerebral cortex3.33e-0822
anatomical group5.49e-08625
vasculature6.68e-0878
vascular system6.68e-0878
neocortex3.51e-0720
vessel5.46e-0768
posterior neural tube7.69e-0715
chordal neural plate7.69e-0715
circulatory system8.74e-07112
compound organ9.15e-0768


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
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
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.18043
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0105.18.55582
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
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.14.04391
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.22.43626
MA0150.13.7809
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.24.43825
MA0079.22.72671
MA0102.21.75932
MA0258.10.418966
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105147.971147625824820.0002476385788090830.00267928369752841
CTCF#1066445.360256373075030.001211145381643620.00816807519782244
EGR1#195844.988179094810140.001615011500076050.0101388666780742
ESR1#2099430.76860329615451.11467714392546e-064.60323314489643e-05
FOS#235348.99795530889440.0001525147711168630.00194748626735225
FOSL1#8061439.7135797163734.01511434669553e-071.93867095355772e-05
FOSL2#2355416.93020060456171.2165416097647e-050.000303377242555434
HDAC8#558691194.1460084033610.005140863901003430.0239028886544786
IRF1#365947.63716375356390.0002938853996185490.00307238210718335
JUN#3725412.51282919233634.07770316866756e-050.000742712314671209
JUNB#3726430.61063265982111.13787152942193e-064.65666789425146e-05
JUND#372746.994663941871030.000417684217818580.00391444023912013
NR3C1#2908414.9730233311731.98868032687801e-050.000442659387593377
RAD21#5885410.35503389545638.6948481184721e-050.00129282637050841
SMARCB1#6598418.25271578115749.00423392720929e-060.000241188301391077
SMARCC1#6599443.66335931963152.74744977017458e-071.40588391252946e-05
SMC3#9126415.04493284493281.95092670935632e-050.000437519507404906
ZNF263#1012748.221841637010680.0002187871180958320.00248611770501693



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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