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Coexpression cluster:C1135: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.100351,0.384703,0.529489,0.90845,0.52784,1.47005,0.643217,0.224331,0.200685,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.28906,1.08139,0.32524,1.00032,0.23059,0.520063,0.897212,0.430372,0.670692,0.957451,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.232776,0.305874,1.3112,0.773034,0.207499,0.829015,0.459366,0.254304,0.902101,0.109128,0.415364,0.60533,0.486696,0.511111,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.921933,0.782748,0.850825,0.424224,0.580264,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.146388,1.69317,1.65172,1.27705,1.01423,0.881388,0.73028,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,1.78098,0.493026,0.815341,0.589207,0.43012,0.873303,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.155979,1.19482,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.76179,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,1.36465,0.738579,1.94751,1.15519,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.877715,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.0992692
|tfbs_overrepresentation_for_novel_motifs=0.392069,0.100351,0.384703,0.529489,0.90845,0.52784,1.47005,0.643217,0.224331,0.200685,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.28906,1.08139,0.32524,1.00032,0.23059,0.520063,0.897212,0.430372,0.670692,0.957451,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.232776,0.305874,1.3112,0.773034,0.207499,0.829015,0.459366,0.254304,0.902101,0.109128,0.415364,0.60533,0.486696,0.511111,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.921933,0.782748,0.850825,0.424224,0.580264,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.146388,1.69317,1.65172,1.27705,1.01423,0.881388,0.73028,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,1.78098,0.493026,0.815341,0.589207,0.43012,0.873303,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.155979,1.19482,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.76179,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,1.36465,0.738579,1.94751,1.15519,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.877715,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.0992692
|tfbs_overrepresentation_jaspar=MA0003.1;0.110456,MA0004.1;0.502801,MA0006.1;0.904424,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0156227,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;2.01466,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;2.03099,MA0031.1;1.8966,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.382278,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.362619,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.575931,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.946606,MA0069.1;2.20119,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.672652,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.252594,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;1.17914,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.918548,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;0.648997,MA0107.1;0.752965,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;1.00897,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.581146,MA0146.1;0.0610556,MA0147.1;0.281049,MA0148.1;1.30922,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.128723,MA0138.2;0.704862,MA0002.2;0.611548,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;1.53797,MA0112.2;0.556641,MA0065.2;0.0828768,MA0150.1;1.10099,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.250175,MA0156.1;0.959643,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.106355,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.07638,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:43, 22 January 2013


Full id: C1135_hippocampus_substantia_thalamus_occipital_locus_medial_brain



Phase1 CAGE Peaks

Hg19::chr11:124793774..124793796,-p10@HEPACAM
Hg19::chr16:19869963..19870000,-p@chr16:19869963..19870000
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Hg19::chr16:19871670..19871687,-p@chr16:19871670..19871687
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Hg19::chr16:19871741..19871755,-p@chr16:19871741..19871755
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Hg19::chr16:19873226..19873239,-p3@GPRC5B
Hg19::chr16:19883175..19883186,-p@chr16:19883175..19883186
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Hg19::chr16:19883313..19883333,-p@chr16:19883313..19883333
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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:0005118sevenless binding0.0121861478021528



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>

Cell Type
Ontology termp-valuen
mesothelial cell2.13e-0819
Uber Anatomy
Ontology termp-valuen
central nervous system2.22e-4981
neural tube1.12e-4856
neural rod1.12e-4856
future spinal cord1.12e-4856
neural keel1.12e-4856
regional part of nervous system3.12e-4453
regional part of brain3.12e-4453
nervous system1.32e-4289
brain3.51e-3868
future brain3.51e-3868
adult organism2.06e-37114
neural plate7.78e-3682
presumptive neural plate7.78e-3682
brain grey matter1.42e-3334
gray matter1.42e-3334
neurectoderm2.15e-3386
telencephalon2.54e-3334
regional part of forebrain4.11e-3341
forebrain4.11e-3341
anterior neural tube4.11e-3341
future forebrain4.11e-3341
regional part of telencephalon1.25e-3032
cerebral hemisphere2.69e-3032
structure with developmental contribution from neural crest6.93e-28132
ecto-epithelium4.12e-26104
cerebral cortex3.44e-2325
pallium3.44e-2325
pre-chordal neural plate2.43e-2161
regional part of cerebral cortex7.50e-2022
neocortex1.65e-1920
ectoderm-derived structure1.95e-19171
ectoderm1.95e-19171
presumptive ectoderm1.95e-19171
tube1.09e-16192
posterior neural tube1.90e-1615
chordal neural plate1.90e-1615
organ system subdivision3.64e-16223
anatomical conduit7.43e-16240
anatomical cluster2.54e-14373
segmental subdivision of hindbrain4.01e-1212
hindbrain4.01e-1212
presumptive hindbrain4.01e-1212
neural nucleus6.52e-129
nucleus of brain6.52e-129
segmental subdivision of nervous system5.55e-1113
epithelium9.78e-11306
cell layer1.96e-10309
gyrus2.76e-106
brainstem3.24e-106
basal ganglion3.93e-099
nuclear complex of neuraxis3.93e-099
aggregate regional part of brain3.93e-099
collection of basal ganglia3.93e-099
cerebral subcortex3.93e-099
telencephalic nucleus5.93e-097
regional part of metencephalon4.27e-089
metencephalon4.27e-089
future metencephalon4.27e-089
multi-tissue structure2.94e-07342


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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.12.01466
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.12.03099
MA0031.11.8966
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.946606
MA0069.12.20119
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.672652
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.11.17914
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.581146
MA0146.10.0610556
MA0147.10.281049
MA0148.11.30922
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.21.53797
MA0112.20.556641
MA0065.20.0828768
MA0150.11.10099
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.250175
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.07638
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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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