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Coexpression cluster:C1372: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,2.90668,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.736703,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,1.06849,0.889639,0.336106,0.236034,0.127969,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.547818,1.31499,0.92701,0.302275,0.225641,0.35719,0.577216,0.35388,0.585658,0.878269,0.248856,0.936389,0.513952,0.664116,0.390088,0.0393783,0.468392,0.66382,0.542147,0.630853,1.02586,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,1.04504,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,1.07049,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,3.87911,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,2.99885,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_for_novel_motifs=0.44418,2.90668,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.736703,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,1.06849,0.889639,0.336106,0.236034,0.127969,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.547818,1.31499,0.92701,0.302275,0.225641,0.35719,0.577216,0.35388,0.585658,0.878269,0.248856,0.936389,0.513952,0.664116,0.390088,0.0393783,0.468392,0.66382,0.542147,0.630853,1.02586,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,1.04504,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,1.07049,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,3.87911,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,2.99885,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_jaspar=MA0003.1;0.00461978,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.0254709,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,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;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;6.79302,MA0055.1;0.808182,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,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;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.120085,MA0074.1;0.660398,MA0076.1;1.19721,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;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;4.66306,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;4.77918,MA0109.1;0,MA0111.1;0.504913,MA0113.1;2.88836,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;1.61362,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;1.15452,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;3.56798,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;0.621793,MA0039.2;0.00570825,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;1.87543,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;1.92418,MA0155.1;0.0961854,MA0156.1;2.81343,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.39622,MA0163.1;0.0270301,MA0164.1;1.74929,MA0080.2;2.70673,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;5.9246e-06,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:53, 22 January 2013


Full id: C1372_liver_Hepatocyte_lung_Melanocyte_hepatocellular_left_prostate



Phase1 CAGE Peaks

Hg19::chr12:9266111..9266133,-p@chr12:9266111..9266133
-
Hg19::chr12:9268445..9268461,-p3@A2M
Hg19::chr12:9268507..9268523,-p1@A2M
Hg19::chr12:9268528..9268542,-p2@A2M
Hg19::chr12:9268547..9268556,-p4@A2M
Hg19::chr12:9268559..9268568,-p5@A2M


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism4.74e-47114
neural tube7.95e-2156
neural rod7.95e-2156
future spinal cord7.95e-2156
neural keel7.95e-2156
regional part of nervous system2.28e-1953
regional part of brain2.28e-1953
central nervous system3.61e-1881
regional part of forebrain2.47e-1741
forebrain2.47e-1741
anterior neural tube2.47e-1741
future forebrain2.47e-1741
organ system subdivision6.67e-16223
brain1.02e-1568
future brain1.02e-1568
nervous system1.52e-1589
telencephalon3.84e-1434
brain grey matter6.30e-1434
gray matter6.30e-1434
neurectoderm1.45e-1386
neural plate1.94e-1382
presumptive neural plate1.94e-1382
regional part of telencephalon3.72e-1332
cerebral hemisphere4.93e-1332
multi-cellular organism1.52e-12656
organ1.26e-11503
structure with developmental contribution from neural crest3.17e-11132
ecto-epithelium7.78e-11104
anatomical cluster1.64e-10373
cerebral cortex3.43e-1025
pallium3.43e-1025
anatomical system5.08e-10624
anatomical group7.04e-10625
regional part of cerebral cortex1.03e-0922
anatomical conduit1.66e-09240
pre-chordal neural plate3.09e-0961
ectoderm-derived structure4.06e-09171
ectoderm4.06e-09171
presumptive ectoderm4.06e-09171
neocortex6.61e-0920
germ layer5.67e-08560
germ layer / neural crest5.67e-08560
embryonic tissue5.67e-08560
presumptive structure5.67e-08560
germ layer / neural crest derived structure5.67e-08560
epiblast (generic)5.67e-08560
tube5.80e-08192
embryonic structure7.04e-08564
multi-tissue structure8.92e-08342
embryo8.25e-07592


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
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
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.16.79302
MA0055.10.808182
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.120085
MA0074.10.660398
MA0076.11.19721
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.14.66306
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.24.77918
MA0109.10
MA0111.10.504913
MA0113.12.88836
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
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.11.15452
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.13.56798
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.21.87543
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.92418
MA0155.10.0961854
MA0156.12.81343
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.10.0270301
MA0164.11.74929
MA0080.22.70673
MA0018.20.709805
MA0099.20.629739
MA0079.25.9246e-06
MA0102.21.58513
MA0258.10.289793
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
ELF1#199753.548414965672950.003446837775721690.0175260121937
EP300#203355.644951438519330.0003688138931814860.00366913261478198
FOXA1#316959.234516457821213.31890114386024e-050.000659731093573696
FOXA2#3170520.52538646055446.3869668268396e-072.91033345736606e-05
HDAC2#3066511.17968353052191.29408913564529e-050.000316889508177393
HEY1#2346264.040111043105710.0002298968555807510.00253031907471789
HNF4A#3172519.27690863579478.72194926701819e-073.78442733484883e-05
HNF4G#3174523.96118543870572.95997618535695e-071.49558274224719e-05
RXRA#6256516.72884761594441.76223204684013e-066.62273309607544e-05
SIN3A#2594254.507403939012610.001096110061208640.007658837136721
SP1#666754.748651148450750.0008523704027326610.00641775737084539
SRF#6722511.49764855180651.12681431027194e-050.000288086559976722
STAT1#6772517.25548958099931.51117799335256e-065.81739470872641e-05
TAF1#687252.785871904787740.01078636340290410.0397879775168967
TBP#690853.088975572580320.006645448275786930.0282833030064351
TCF7L2#693458.975147135947793.818060286338e-050.000719903228461554



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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