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Coexpression cluster:C1202: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.0232809,0.384703,0.529489,0.90845,0.52784,0.604235,0.643217,0.224331,0.443077,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.28906,0.19568,0.32524,0.384762,0.0646572,0.520063,0.338096,0.430372,0.670692,0.49486,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.0934825,0.305874,0.529001,0.773034,0.207499,0.829015,0.459366,0.921877,0.340293,0.0257952,0.415364,0.60533,0.486696,0.876276,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.638689,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,1.90083,0.115253,1.0929,0.179863,0.168304,0.156354,0.782748,1.98123,1.0864,1.099,0.798651,0.625403,0.649554,1.04131,0.310394,0.322252,0.448771,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.566252,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,1.23455,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.988112,0.507004,1.22894,0.304323,0.358137,0.474472,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.433733,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.877715,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,1.46724,0.00626991
|tfbs_overrepresentation_jaspar=MA0003.1;0.00215847,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0156227,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,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;1.22833,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.649431,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.0282921,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;0.0723293,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,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;0.388712,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;0.547495,MA0140.1;1.38735,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.0807715,MA0146.1;0.0127148,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.00276064,MA0138.2;0.704862,MA0002.2;0.611548,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.25944,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;1.40221,MA0079.2;9.11084e-05,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:46, 22 January 2013


Full id: C1202_hippocampus_amygdala_medial_middle_parietal_pons_insula



Phase1 CAGE Peaks

Hg19::chr14:70234642..70234664,+p17@SRSF5
Hg19::chr15:80733538..80733547,+p23@ARNT2
Hg19::chr5:153191119..153191132,+p11@GRIA1
Hg19::chr5:22754587..22754623,+p@chr5:22754587..22754623
+
Hg19::chr6:95445637..95445675,-p@chr6:95445637..95445675
-
Hg19::chrX:85218889..85218912,-p@chrX:85218889..85218912
-
Hg19::chrX:85218927..85218946,-p@chrX:85218927..85218946
-


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:0017162aryl hydrocarbon receptor binding0.00718217406696926
GO:0005061aryl hydrocarbon receptor nuclear translocator activity0.00718217406696926
GO:0004971alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity0.00718217406696926
GO:0015277kainate selective glutamate receptor activity0.0143632909991038
GO:0004970ionotropic glutamate receptor activity0.0448575345827884
GO:0005234extracellular-glutamate-gated ion channel activity0.0448575345827884
GO:0001666response to hypoxia0.0448575345827884
GO:0001701in utero embryonic development0.0448575345827884



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
brain grey matter4.33e-9634
gray matter4.33e-9634
neural tube8.08e-9556
neural rod8.08e-9556
future spinal cord8.08e-9556
neural keel8.08e-9556
regional part of nervous system4.19e-9453
regional part of brain4.19e-9453
cerebral hemisphere5.54e-9432
telencephalon2.50e-8834
regional part of telencephalon2.99e-8632
regional part of forebrain1.58e-8541
forebrain1.58e-8541
anterior neural tube1.58e-8541
future forebrain1.58e-8541
regional part of cerebral cortex5.66e-7722
brain2.84e-7668
future brain2.84e-7668
central nervous system4.26e-7281
cerebral cortex1.21e-6725
pallium1.21e-6725
neocortex3.82e-6620
nervous system1.85e-6489
neural plate2.79e-6382
presumptive neural plate2.79e-6382
neurectoderm4.24e-6086
pre-chordal neural plate3.17e-5661
adult organism7.65e-51114
ecto-epithelium8.89e-49104
structure with developmental contribution from neural crest5.74e-40132
gyrus4.16e-346
ectoderm-derived structure3.27e-31171
ectoderm3.27e-31171
presumptive ectoderm3.27e-31171
basal ganglion8.97e-309
nuclear complex of neuraxis8.97e-309
aggregate regional part of brain8.97e-309
collection of basal ganglia8.97e-309
cerebral subcortex8.97e-309
limbic system2.10e-295
neural nucleus3.28e-299
nucleus of brain3.28e-299
organ system subdivision3.54e-24223
tube8.93e-24192
brainstem9.55e-236
temporal lobe8.17e-216
telencephalic nucleus1.45e-197
parietal lobe2.45e-185
frontal cortex4.61e-183
anatomical conduit8.22e-18240
pons1.29e-173
organ part7.00e-16218
corpus striatum3.48e-134
striatum3.48e-134
ventral part of telencephalon3.48e-134
future corpus striatum3.48e-134
Ammon's horn4.14e-132
lobe parts of cerebral cortex4.14e-132
hippocampal formation4.14e-132
limbic lobe4.14e-132
middle temporal gyrus6.25e-132
amygdala7.44e-132
middle frontal gyrus9.39e-132
epithelium1.22e-12306
posterior neural tube1.27e-1215
chordal neural plate1.27e-1215
cell layer1.86e-12309
locus ceruleus4.15e-122
brainstem nucleus4.15e-122
hindbrain nucleus4.15e-122
anatomical cluster5.21e-12373
globus pallidus8.11e-122
pallidum8.11e-122
segmental subdivision of hindbrain2.74e-1112
hindbrain2.74e-1112
presumptive hindbrain2.74e-1112
multi-tissue structure1.23e-10342
occipital lobe1.66e-105
segmental subdivision of nervous system2.10e-1013
caudate-putamen2.16e-083
dorsal striatum2.16e-083
medulla oblongata6.04e-083
myelencephalon6.04e-083
future myelencephalon6.04e-083
insula3.36e-071
olfactory region4.51e-071
primary subdivision of skull4.51e-071
cranium4.51e-071
neurocranium4.51e-071
chondrocranium4.51e-071
cartilaginous neurocranium4.51e-071
head paraxial mesoderm4.51e-071
nucleus accumbens6.02e-071
ventral striatum6.02e-071
postcentral gyrus7.15e-071
putamen7.57e-071
paracentral gyrus8.98e-071


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.11.22833
MA0051.10.602745
MA0052.10.896548
MA0055.10.649431
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0282921
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.11.38735
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.25944
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.21.40221
MA0079.29.11084e-05
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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