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Coexpression cluster:C1127: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.01633,0.465735,0.384703,0.529489,1.62733,0.52784,0.604235,0.226729,0.224331,0.443077,0.497563,0.647852,1.03506,0.592674,0.341795,0.365029,0.827563,0.28906,0.19568,0.32524,0.384762,0.23059,0.520063,0.897212,0.430372,2.71467,0.164928,0.517892,0.346214,0.150685,0.475674,0.864517,0.714156,0.546594,0.309012,0.021349,2.27897,0.529001,0.282922,1.12779,0.307642,0.459366,0.541549,0.340293,0.0257952,1.06715,0.60533,0.486696,0.876276,0.346342,0.684981,1.49721,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,1.13397,0.232216,1.2198,1.0929,0.179863,0.971313,0.156354,0.782748,0.850825,1.90717,1.099,0.798651,2.56965,0.229431,1.04131,0.567403,1.62218,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.194299,2.13136,0.715799,0.413337,0.28424,0.875714,0.918549,0.831244,1.78098,0.493026,0.815341,0.589207,0.43012,1.57162,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.642446,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,2.59532,1.28996,1.37933,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.722945,0.106334,0.518684,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.695791,0.602897,0.0992692
|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;0.610358,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;1.29551,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.766755,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.158296,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;0.0022316,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;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;0.695228,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;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.276317,MA0146.1;0.0610556,MA0147.1;0.281049,MA0148.1;1.30922,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;1.38583,MA0039.2;0.128723,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;1.53797,MA0112.2;0.262665,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;0.485816,MA0163.1;0.0765396,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.0441319,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: C1127_cerebellum_substantia_spinal_thalamus_medulla_occipital_globus



Phase1 CAGE Peaks

Hg19::chr11:105948129..105948161,-p2@KBTBD3
Hg19::chr17:36729056..36729072,-p8@SRCIN1
Hg19::chr17:66201593..66201646,+p@chr17:66201593..66201646
+
Hg19::chr1:171911363..171911369,+p@chr1:171911363..171911369
+
Hg19::chr3:129407466..129407477,-p19@TMCC1
Hg19::chr3:129407485..129407505,-p5@TMCC1
Hg19::chr3:129407535..129407543,-p21@TMCC1


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
embryonic stem cell3.34e-085
Uber Anatomy
Ontology termp-valuen
neural tube1.17e-7756
neural rod1.17e-7756
future spinal cord1.17e-7756
neural keel1.17e-7756
regional part of nervous system4.60e-7253
regional part of brain4.60e-7253
adult organism2.22e-67114
central nervous system1.37e-6681
nervous system5.19e-6589
regional part of forebrain1.42e-5941
forebrain1.42e-5941
anterior neural tube1.42e-5941
future forebrain1.42e-5941
neural plate2.19e-5982
presumptive neural plate2.19e-5982
brain3.71e-5768
future brain3.71e-5768
neurectoderm7.94e-5686
brain grey matter2.15e-4734
gray matter2.15e-4734
telencephalon3.10e-4734
ecto-epithelium6.18e-45104
regional part of telencephalon1.43e-4332
cerebral hemisphere1.98e-4332
pre-chordal neural plate8.51e-4361
structure with developmental contribution from neural crest3.28e-37132
organ system subdivision2.24e-34223
regional part of cerebral cortex2.15e-3322
cerebral cortex1.92e-3125
pallium1.92e-3125
ectoderm-derived structure2.86e-31171
ectoderm2.86e-31171
presumptive ectoderm2.86e-31171
neocortex5.44e-3020
tube8.95e-25192
posterior neural tube2.28e-1815
chordal neural plate2.28e-1815
anatomical conduit9.02e-18240
anatomical cluster9.15e-18373
neural nucleus1.30e-179
nucleus of brain1.30e-179
basal ganglion3.84e-179
nuclear complex of neuraxis3.84e-179
aggregate regional part of brain3.84e-179
collection of basal ganglia3.84e-179
cerebral subcortex3.84e-179
segmental subdivision of nervous system5.67e-1513
epithelium2.84e-14306
cell layer6.01e-14309
telencephalic nucleus8.30e-147
diencephalon1.31e-137
future diencephalon1.31e-137
segmental subdivision of hindbrain2.42e-1312
hindbrain2.42e-1312
presumptive hindbrain2.42e-1312
brainstem9.33e-136
multi-tissue structure3.27e-12342
gyrus4.12e-126
organ part1.56e-10218
parietal lobe3.30e-105
limbic system4.55e-105
occipital lobe5.58e-105
embryo2.53e-09592
regional part of metencephalon2.15e-089
metencephalon2.15e-089
future metencephalon2.15e-089
corpus striatum2.82e-084
striatum2.82e-084
ventral part of telencephalon2.82e-084
future corpus striatum2.82e-084
regional part of diencephalon3.04e-084
organ3.22e-08503
gland of diencephalon4.09e-084
neuroendocrine gland4.09e-084
germ layer9.88e-08560
germ layer / neural crest9.88e-08560
embryonic tissue9.88e-08560
presumptive structure9.88e-08560
germ layer / neural crest derived structure9.88e-08560
epiblast (generic)9.88e-08560
embryonic structure1.63e-07564
multi-cellular organism2.18e-07656
pons2.64e-073
medulla oblongata4.17e-073
myelencephalon4.17e-073
future myelencephalon4.17e-073
developing anatomical structure4.87e-07581
spinal cord6.04e-073
dorsal region element6.04e-073
dorsum6.04e-073
temporal lobe6.37e-076
frontal cortex6.79e-073


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
MA0014.10.610358
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
MA0041.11.29551
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
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
MA0073.10.0022316
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
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.695228
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
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.0610556
MA0147.10.281049
MA0148.11.30922
MA0149.10.555119
MA0062.20.193221
MA0035.21.38583
MA0039.20.128723
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.21.53797
MA0112.20.262665
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
MA0162.10.485816
MA0163.10.0765396
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.0441319
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

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

TF#promotersEnrichmentp-valueq-value
FOXA1#316946.332239856791690.001854681016920170.0109423246371102
HEY1#2346252.885793602218360.01231366941853030.0446196419541282
NANOG#79923312.53347649186260.001261052189503470.00846801450649734
NRF1#489946.977302541549090.00128531428862220.00861874407636685



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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