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Coexpression cluster:C355: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0423165,1.9414,0.156056,0.663734,0.833138,1.09711,1.35804,4.56441,0.106216,0.0681302,0.082933,0.16234,0.272058,0.8119,0.518813,0.920836,0.283109,0.0163503,1.32897,0.921334,0.0400195,1.11899,0.0933127,0.113236,0.0554737,0.176305,2.0953,1.06392,0.845317,1.22449,0.255613,0.310643,2.3291,1.2453,0.224873,0.00668186,0.0196487,0.0975929,0.184446,0.00523109,0.0200166,0.508948,0.0328443,0.115116,1.35814,0.418148,0.426563,0.078127,0.0568324,1.22376,0.185267,0.144315,1.14162,0.370484,0.497309,0.818987,0.124075,0.114516,3.13613,0.365802,0.342179,0.138926,1.22129,0.262912,0.14927,0.670778,0.574343,0.913986,0.302792,0.761456,0.0614495,0.00779031,0.184789,0.495593,0.0602122,0.118769,0.729017,0.250834,0.300348,0.43599,0.754548,1.33527,0.149063,0.11227,0.451923,3.38174e-05,0.0101403,0.0341816,0.584976,1.00897,0.65804,0.429389,0.323471,1.13902,0.0284506,1.21862,2.06929,0.356655,0.592226,0.000965535,0.186412,0.319139,0.352258,0.779618,1.21654,0.0809099,0.27418,0.128645,0.0553809,0.0243978,0.379768,0.350081,2.97687,0.0872186,0.614737,0.682395,7.84401e-05,0.0728865,0.236884,0.0604617,0.488501,0.200525,0.0957026,0.155712,0.715288,0.251373,0.133408,0.327313,0.525232,0.584302,1.09885,0.0746108,0.537753,0.153736,0.669744,0.155732,3.79803,0.638657,0.631317,1.45283,1.05945,0.597865,0.134374,0.353873,2.66529,2.35641,0.220337,1.29622,0.0653198,0.153084,0.0375216,6.56022e-05,0.430278,0.0975287,0.138651,0.789951,0.191579,0.105897,1.19251,1.51599,0.596781,0.414981,0.299757,0.703182,0.242939,0.454322,0.0498652,1.35339,1.60584
|tfbs_overrepresentation_for_novel_motifs=0.0423165,1.9414,0.156056,0.663734,0.833138,1.09711,1.35804,4.56441,0.106216,0.0681302,0.082933,0.16234,0.272058,0.8119,0.518813,0.920836,0.283109,0.0163503,1.32897,0.921334,0.0400195,1.11899,0.0933127,0.113236,0.0554737,0.176305,2.0953,1.06392,0.845317,1.22449,0.255613,0.310643,2.3291,1.2453,0.224873,0.00668186,0.0196487,0.0975929,0.184446,0.00523109,0.0200166,0.508948,0.0328443,0.115116,1.35814,0.418148,0.426563,0.078127,0.0568324,1.22376,0.185267,0.144315,1.14162,0.370484,0.497309,0.818987,0.124075,0.114516,3.13613,0.365802,0.342179,0.138926,1.22129,0.262912,0.14927,0.670778,0.574343,0.913986,0.302792,0.761456,0.0614495,0.00779031,0.184789,0.495593,0.0602122,0.118769,0.729017,0.250834,0.300348,0.43599,0.754548,1.33527,0.149063,0.11227,0.451923,3.38174e-05,0.0101403,0.0341816,0.584976,1.00897,0.65804,0.429389,0.323471,1.13902,0.0284506,1.21862,2.06929,0.356655,0.592226,0.000965535,0.186412,0.319139,0.352258,0.779618,1.21654,0.0809099,0.27418,0.128645,0.0553809,0.0243978,0.379768,0.350081,2.97687,0.0872186,0.614737,0.682395,7.84401e-05,0.0728865,0.236884,0.0604617,0.488501,0.200525,0.0957026,0.155712,0.715288,0.251373,0.133408,0.327313,0.525232,0.584302,1.09885,0.0746108,0.537753,0.153736,0.669744,0.155732,3.79803,0.638657,0.631317,1.45283,1.05945,0.597865,0.134374,0.353873,2.66529,2.35641,0.220337,1.29622,0.0653198,0.153084,0.0375216,6.56022e-05,0.430278,0.0975287,0.138651,0.789951,0.191579,0.105897,1.19251,1.51599,0.596781,0.414981,0.299757,0.703182,0.242939,0.454322,0.0498652,1.35339,1.60584
|tfbs_overrepresentation_jaspar=MA0003.1;0.0544996,MA0004.1;0.085298,MA0006.1;0.116014,MA0007.1;0.0768943,MA0009.1;0.395891,MA0014.1;0.00277835,MA0017.1;0.350881,MA0019.1;0.165418,MA0024.1;0.312615,MA0025.1;0.508683,MA0027.1;1.93196,MA0028.1;0.130296,MA0029.1;0.327543,MA0030.1;0.318663,MA0031.1;0.270046,MA0038.1;0.138548,MA0040.1;0.332103,MA0041.1;4.26959,MA0042.1;0.272024,MA0043.1;0.39615,MA0046.1;0.386991,MA0048.1;0.684374,MA0050.1;0.273123,MA0051.1;0.422881,MA0052.1;0.335128,MA0055.1;1.48126,MA0056.1;0,MA0057.1;0.0170157,MA0058.1;0.0469637,MA0059.1;0.0465255,MA0060.1;0.226068,MA0061.1;0.0254374,MA0063.1;0,MA0066.1;0.138793,MA0067.1;0.673046,MA0068.1;0.00211477,MA0069.1;0.383853,MA0070.1;0.374777,MA0071.1;0.752373,MA0072.1;1.72513,MA0073.1;2.12364e-06,MA0074.1;0.135707,MA0076.1;0.756572,MA0077.1;0.364942,MA0078.1;0.573222,MA0081.1;0.397764,MA0083.1;0.40206,MA0084.1;0.847335,MA0087.1;0.369175,MA0088.1;0.803162,MA0089.1;0,MA0090.1;2.25281,MA0091.1;0.292177,MA0092.1;0.0698409,MA0093.1;0.0285794,MA0095.1;0,MA0098.1;0,MA0100.1;0.146599,MA0101.1;0.121552,MA0103.1;0.789368,MA0105.1;0.0125892,MA0106.1;0.163029,MA0107.1;0.0650129,MA0108.2;0.267801,MA0109.1;0,MA0111.1;0.845209,MA0113.1;1.57449,MA0114.1;1.169,MA0115.1;0.603788,MA0116.1;0.348601,MA0117.1;0.427006,MA0119.1;0.0412526,MA0122.1;0.44876,MA0124.1;0.566745,MA0125.1;0.493194,MA0130.1;0,MA0131.1;1.13481,MA0132.1;0,MA0133.1;0,MA0135.1;0.420972,MA0136.1;0.863999,MA0139.1;1.97585,MA0140.1;2.41691,MA0141.1;0.17465,MA0142.1;1.27897,MA0143.1;0.173319,MA0144.1;1.44648,MA0145.1;1.16026,MA0146.1;0.842302,MA0147.1;0.181668,MA0148.1;0.0971411,MA0149.1;0.110599,MA0062.2;0.0234822,MA0035.2;2.41286,MA0039.2;0.000320891,MA0138.2;0.575161,MA0002.2;0.8313,MA0137.2;0.3196,MA0104.2;0.105762,MA0047.2;0.155654,MA0112.2;1.08009,MA0065.2;0.547406,MA0150.1;0.783414,MA0151.1;0,MA0152.1;0.119196,MA0153.1;0.478697,MA0154.1;1.22579,MA0155.1;0.121291,MA0156.1;1.32801,MA0157.1;0.227782,MA0158.1;0,MA0159.1;0.0700275,MA0160.1;1.14983,MA0161.1;0,MA0162.1;1.15999e-05,MA0163.1;0.0553725,MA0164.1;1.02316,MA0080.2;0.838393,MA0018.2;0.163878,MA0099.2;0.119388,MA0079.2;8.16063e-09,MA0102.2;0.88257,MA0258.1;1.7713,MA0259.1;0.0164145,MA0442.1;0
}}
}}

Revision as of 19:06, 22 January 2013


Full id: C355_Chondrocyte_Hepatocyte_spinal_medulla_cerebral_seminal_hippocampus



Phase1 CAGE Peaks

Hg19::chr8:27455536..27455576,-p@chr8:27455536..27455576
-
Hg19::chr8:27455583..27455667,-p@chr8:27455583..27455667
-
Hg19::chr8:27455692..27455710,-p@chr8:27455692..27455710
-
Hg19::chr8:27455711..27455732,-p@chr8:27455711..27455732
-
Hg19::chr8:27456058..27456137,-p@chr8:27456058..27456137
-
Hg19::chr8:27456141..27456161,-p@chr8:27456141..27456161
-
Hg19::chr8:27457336..27457372,-p@chr8:27457336..27457372
-
Hg19::chr8:27457396..27457456,-p@chr8:27457396..27457456
-
Hg19::chr8:27457470..27457493,-p@chr8:27457470..27457493
-
Hg19::chr8:27457494..27457531,-p@chr8:27457494..27457531
-
Hg19::chr8:27461872..27461920,-p@chr8:27461872..27461920
-
Hg19::chr8:27462566..27462587,-p24@CLU
Hg19::chr8:27462617..27462687,-p9@CLU
Hg19::chr8:27462692..27462746,-p14@CLU
Hg19::chr8:27462747..27462758,-p31@CLU
Hg19::chr8:27462773..27462781,-p28@CLU
Hg19::chr8:27462787..27462819,-p20@CLU
Hg19::chr8:27462822..27462853,-p10@CLU
Hg19::chr8:27463908..27463929,-p18@CLU
Hg19::chr8:27463932..27463992,-p4@CLU
Hg19::chr8:27463995..27464033,-p15@CLU
Hg19::chr8:27464034..27464046,-p25@CLU
Hg19::chr8:27466494..27466506,-p17@CLU
Hg19::chr8:27466535..27466550,-p5@CLU
Hg19::chr8:27466559..27466562,-p44@CLU
Hg19::chr8:27466559..27466566,+p@chr8:27466559..27466566
+
Hg19::chr8:27466577..27466595,-p8@CLU
Hg19::chr8:27466597..27466608,-p23@CLU
Hg19::chr8:27468013..27468046,-p6@CLU
Hg19::chr8:27468052..27468067,-p13@CLU
Hg19::chr8:27468075..27468130,-p7@CLU
Hg19::chr8:27472209..27472225,-p1@CLU


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 organism8.25e-53114
neural tube9.93e-3956
neural rod9.93e-3956
future spinal cord9.93e-3956
neural keel9.93e-3956
central nervous system5.71e-3781
regional part of nervous system4.11e-3653
regional part of brain4.11e-3653
nervous system3.19e-3289
neural plate3.70e-3282
presumptive neural plate3.70e-3282
brain9.32e-3168
future brain9.32e-3168
neurectoderm3.19e-2986
regional part of forebrain1.72e-2841
forebrain1.72e-2841
anterior neural tube1.72e-2841
future forebrain1.72e-2841
brain grey matter1.09e-2434
gray matter1.09e-2434
telencephalon2.57e-2434
organ system subdivision2.99e-24223
regional part of telencephalon4.10e-2332
cerebral hemisphere6.26e-2332
pre-chordal neural plate1.25e-2161
ecto-epithelium3.12e-20104
structure with developmental contribution from neural crest1.05e-18132
cerebral cortex2.87e-1825
pallium2.87e-1825
anatomical cluster6.50e-17373
regional part of cerebral cortex1.50e-1622
ectoderm-derived structure3.19e-16171
ectoderm3.19e-16171
presumptive ectoderm3.19e-16171
neocortex6.15e-1520
anatomical conduit3.17e-11240
posterior neural tube3.55e-1115
chordal neural plate3.55e-1115
organ part2.24e-10218
tube3.52e-10192
segmental subdivision of nervous system2.80e-0913
organ8.30e-09503
segmental subdivision of hindbrain9.77e-0912
hindbrain9.77e-0912
presumptive hindbrain9.77e-0912
multi-tissue structure1.59e-08342
multi-cellular organism2.25e-08656
basal ganglion6.34e-089
nuclear complex of neuraxis6.34e-089
aggregate regional part of brain6.34e-089
collection of basal ganglia6.34e-089
cerebral subcortex6.34e-089
neural nucleus7.28e-089
nucleus of brain7.28e-089
anatomical system4.03e-07624
anatomical group5.21e-07625


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)
MA0003.10.0544996
MA0004.10.085298
MA0006.10.116014
MA0007.10.0768943
MA0009.10.395891
MA0014.10.00277835
MA0017.10.350881
MA0019.10.165418
MA0024.10.312615
MA0025.10.508683
MA0027.11.93196
MA0028.10.130296
MA0029.10.327543
MA0030.10.318663
MA0031.10.270046
MA0038.10.138548
MA0040.10.332103
MA0041.14.26959
MA0042.10.272024
MA0043.10.39615
MA0046.10.386991
MA0048.10.684374
MA0050.10.273123
MA0051.10.422881
MA0052.10.335128
MA0055.11.48126
MA0056.10
MA0057.10.0170157
MA0058.10.0469637
MA0059.10.0465255
MA0060.10.226068
MA0061.10.0254374
MA0063.10
MA0066.10.138793
MA0067.10.673046
MA0068.10.00211477
MA0069.10.383853
MA0070.10.374777
MA0071.10.752373
MA0072.11.72513
MA0073.12.12364e-06
MA0074.10.135707
MA0076.10.756572
MA0077.10.364942
MA0078.10.573222
MA0081.10.397764
MA0083.10.40206
MA0084.10.847335
MA0087.10.369175
MA0088.10.803162
MA0089.10
MA0090.12.25281
MA0091.10.292177
MA0092.10.0698409
MA0093.10.0285794
MA0095.10
MA0098.10
MA0100.10.146599
MA0101.10.121552
MA0103.10.789368
MA0105.10.0125892
MA0106.10.163029
MA0107.10.0650129
MA0108.20.267801
MA0109.10
MA0111.10.845209
MA0113.11.57449
MA0114.11.169
MA0115.10.603788
MA0116.10.348601
MA0117.10.427006
MA0119.10.0412526
MA0122.10.44876
MA0124.10.566745
MA0125.10.493194
MA0130.10
MA0131.11.13481
MA0132.10
MA0133.10
MA0135.10.420972
MA0136.10.863999
MA0139.11.97585
MA0140.12.41691
MA0141.10.17465
MA0142.11.27897
MA0143.10.173319
MA0144.11.44648
MA0145.11.16026
MA0146.10.842302
MA0147.10.181668
MA0148.10.0971411
MA0149.10.110599
MA0062.20.0234822
MA0035.22.41286
MA0039.20.000320891
MA0138.20.575161
MA0002.20.8313
MA0137.20.3196
MA0104.20.105762
MA0047.20.155654
MA0112.21.08009
MA0065.20.547406
MA0150.10.783414
MA0151.10
MA0152.10.119196
MA0153.10.478697
MA0154.11.22579
MA0155.10.121291
MA0156.11.32801
MA0157.10.227782
MA0158.10
MA0159.10.0700275
MA0160.11.14983
MA0161.10
MA0162.11.15999e-05
MA0163.10.0553725
MA0164.11.02316
MA0080.20.838393
MA0018.20.163878
MA0099.20.119388
MA0079.28.16063e-09
MA0102.20.88257
MA0258.11.7713
MA0259.10.0164145
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

No analysis results for this cluster

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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