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Coexpression cluster:C1502: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.603698,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.267027,0.555913,0.553339,0.707204,0.635275,0.650887,0.391663,1.06849,0.889639,0.336106,1.92111,1.30166,0.436569,1.03374,0.576478,0.387783,0.483957,0.730467,1.10781,0.574247,0.396295,1.04549,0.530785,0.92701,2.26105,0.225641,1.67655,0.0334022,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,1.89526,0.468392,0.66382,0.542147,0.0909286,1.02586,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,1.04504,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.75612,0.146905,1.15727,1.17153,0.206105,1.68655,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,2.11086,1.10535,1.10459,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.80351,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,2.16032,3.68759,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,1.13818,0.978783,0.430775,1.38333,1.29401,0.928633,2.8488,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,1.58249,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.826087,0.8388,0.639143,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,2.00817,1.27379,1.06043,0.912368,2.01935,0.83286,0.683502,0.29379,0.661335,2.36361
|tfbs_overrepresentation_jaspar=MA0003.1;1.04263,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.491287,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;1.05129,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;0.464411,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.213007,MA0056.1;0,MA0057.1;0.147053,MA0058.1;1.16137,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;1.72313,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;1.2326,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.660742,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;1.02138,MA0095.1;0,MA0098.1;0,MA0100.1;2.74425,MA0101.1;0.397846,MA0103.1;0.993014,MA0105.1;0.419295,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;8.36196,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;5.48302,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.354331,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.819655,MA0155.1;1.09123,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;1.46233,MA0161.1;0,MA0162.1;2.97671,MA0163.1;1.60684,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;5.1832,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:58, 22 January 2013


Full id: C1502_mature_Hepatocyte_argyrophil_hepatoblastoma_liver_hepatocellular_Adipocyte



Phase1 CAGE Peaks

Hg19::chr2:216946482..216946499,-p2@PECR
Hg19::chr7:73038839..73038862,-p1@MLXIPL
Hg19::chr7:73038865..73038866,-p4@MLXIPL
Hg19::chr7:73038867..73038878,-p2@MLXIPL
Hg19::chr7:73038889..73038905,-p3@MLXIPL
Hg19::chr9:130659627..130659649,-p6@ST6GALNAC6


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

GO IDGO nameFDR corrected p-value
GO:0019166trans-2-enoyl-CoA reductase (NADPH) activity0.0174844729335235



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
fat cell3.99e-0715
Uber Anatomy
Ontology termp-valuen
adult organism7.08e-39114
organ system subdivision2.80e-26223
neural tube2.63e-2156
neural rod2.63e-2156
future spinal cord2.63e-2156
neural keel2.63e-2156
regional part of nervous system2.81e-2053
regional part of brain2.81e-2053
nervous system2.54e-1789
central nervous system1.65e-1681
regional part of forebrain2.15e-1641
forebrain2.15e-1641
anterior neural tube2.15e-1641
future forebrain2.15e-1641
brain7.96e-1668
future brain7.96e-1668
neurectoderm3.82e-1586
neural plate2.51e-1482
presumptive neural plate2.51e-1482
brain grey matter8.53e-1334
gray matter8.53e-1334
telencephalon1.60e-1234
cerebral hemisphere4.74e-1232
regional part of telencephalon1.18e-1132
anatomical cluster1.24e-11373
regional part of cerebral cortex1.45e-1122
subdivision of digestive tract6.16e-11118
ecto-epithelium9.55e-11104
neocortex1.66e-1020
pre-chordal neural plate2.31e-1061
multi-tissue structure1.50e-09342
cerebral cortex2.09e-0925
pallium2.09e-0925
ectoderm-derived structure1.56e-08171
ectoderm1.56e-08171
presumptive ectoderm1.56e-08171
organ2.80e-08503
digestive system5.28e-08145
digestive tract5.28e-08145
primitive gut5.28e-08145
tube5.97e-08192
anatomical conduit1.35e-07240
foregut2.56e-0787
structure with developmental contribution from neural crest3.19e-07132
immaterial anatomical entity6.95e-07117
Disease
Ontology termp-valuen
cell type cancer3.76e-14143
carcinoma1.77e-13106


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)
MA0003.11.04263
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
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
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.147053
MA0058.11.16137
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.72313
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.11.2326
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.12.74425
MA0101.10.397846
MA0103.10.993014
MA0105.10.419295
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
MA0146.18.36196
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.25.48302
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.11.09123
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.11.46233
MA0161.10
MA0162.12.97671
MA0163.11.60684
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.25.1832
MA0102.21.58513
MA0258.10.788656
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

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

TF#promotersEnrichmentp-valueq-value
CCNT2#90544.224134384641760.007109805478875810.0296163439058835
E2F4#187448.445373543522960.0005111193523770840.00443398903919846
E2F6#187654.180963109747820.001573598759586970.00997542220652524
HEY1#2346264.040111043105710.0002298968555807510.00253379038623871
HMGN3#932445.452365148900390.002729616882333770.0149891402057972
IRF1#365945.091442502375930.003535240765893810.0179458058884603
POLR2A#543062.147453176558070.01019570676818780.0380581657372589
SIN3A#2594254.507403939012610.001096110061208640.00766139999214086
SREBF1#6720431.33723296032552.9644579358811e-060.000101376890100028
TAF1#687263.343046285745290.0007162474284635620.0057356360359842
TBP#690863.706770687096390.000385416472907960.00378064346896163



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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