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Coexpression cluster:C702: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.21158,1.46688,0.635061,0.345441,0.556358,0.344001,1.05908,0.340819,0.102889,1.10395,0.317729,0.451026,0.949576,0.401301,0.189126,0.207465,0.617549,0.148925,0.0839658,0.533397,0.635173,0.069487,0.337221,0.546841,2.05043,1.18915,0.231222,0.335332,1.06915,0.206722,0.809412,1.57102,0.12577,0.268295,0.163884,2.13197,2.15638,0.345014,0.14439,1.56694,0.162847,0.777985,0.20746,0.187953,0.912793,0.693545,0.412635,0.308385,0.369629,0.562381,0.484909,1.08437,0.347648,0.725869,0.873575,1.04226,0.195993,0.374657,1.20369,0.976149,2.78101,0.414771,0.688915,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.752663,0.108268,1.37888,0.871629,1.39323,0.874985,0.216432,0.575479,0.639503,1.31112,0.0868483,0.590372,0.4307,0.10636,0.821696,1.76111,1.65013,1.17597,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,0.557745,0.140087,1.48453,0.709167,0.51326,0.0463096,0.875673,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,0.398205,0.260543,1.01047,0.232335,0.701175,0.21882,0.325885,1.00416,0.16034,3.93425,0.297931,0.556847,0.414358,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.434621,0.796235,0.301402,0.919079,0.437919,1.06395,1.13627,0.293853,0.335825,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,1.40937,0.802925,1.29793,1.70437,0.796604,0.663597,0.414334,1.19239,0.494,0.179455,0.260802,0.237047,0.984474,0.778717,0.638755,1.94035,0.564971,0.429983,0.381825,1.86032,0.51183
|tfbs_overrepresentation_for_novel_motifs=1.21158,1.46688,0.635061,0.345441,0.556358,0.344001,1.05908,0.340819,0.102889,1.10395,0.317729,0.451026,0.949576,0.401301,0.189126,0.207465,0.617549,0.148925,0.0839658,0.533397,0.635173,0.069487,0.337221,0.546841,2.05043,1.18915,0.231222,0.335332,1.06915,0.206722,0.809412,1.57102,0.12577,0.268295,0.163884,2.13197,2.15638,0.345014,0.14439,1.56694,0.162847,0.777985,0.20746,0.187953,0.912793,0.693545,0.412635,0.308385,0.369629,0.562381,0.484909,1.08437,0.347648,0.725869,0.873575,1.04226,0.195993,0.374657,1.20369,0.976149,2.78101,0.414771,0.688915,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.752663,0.108268,1.37888,0.871629,1.39323,0.874985,0.216432,0.575479,0.639503,1.31112,0.0868483,0.590372,0.4307,0.10636,0.821696,1.76111,1.65013,1.17597,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,0.557745,0.140087,1.48453,0.709167,0.51326,0.0463096,0.875673,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,0.398205,0.260543,1.01047,0.232335,0.701175,0.21882,0.325885,1.00416,0.16034,3.93425,0.297931,0.556847,0.414358,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.434621,0.796235,0.301402,0.919079,0.437919,1.06395,1.13627,0.293853,0.335825,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,1.40937,0.802925,1.29793,1.70437,0.796604,0.663597,0.414334,1.19239,0.494,0.179455,0.260802,0.237047,0.984474,0.778717,0.638755,1.94035,0.564971,0.429983,0.381825,1.86032,0.51183
|tfbs_overrepresentation_jaspar=MA0003.1;0.881315,MA0004.1;0.32225,MA0006.1;0.188769,MA0007.1;0.305951,MA0009.1;0.756202,MA0014.1;2.20911,MA0017.1;0.627635,MA0019.1;0.45566,MA0024.1;0.654931,MA0025.1;0.886436,MA0027.1;2.35633,MA0028.1;0.201461,MA0029.1;0.673506,MA0030.1;0.662482,MA0031.1;0.600685,MA0038.1;0.414169,MA0040.1;0.67914,MA0041.1;0.338572,MA0042.1;0.310552,MA0043.1;0.756508,MA0046.1;0.745626,MA0048.1;0.641892,MA0050.1;0.837296,MA0051.1;0.410316,MA0052.1;0.682867,MA0055.1;0.901232,MA0056.1;0,MA0057.1;1.38004,MA0058.1;0.240796,MA0059.1;0.239727,MA0060.1;0.337131,MA0061.1;0.28989,MA0063.1;0,MA0066.1;0.414559,MA0067.1;1.06751,MA0068.1;0.226673,MA0069.1;0.741884,MA0070.1;0.731026,MA0071.1;0.379038,MA0072.1;0.726666,MA0073.1;7.64865,MA0074.1;0.40963,MA0076.1;0.254045,MA0077.1;1.70983,MA0078.1;1.25378,MA0081.1;0.239862,MA0083.1;0.763502,MA0084.1;1.25286,MA0087.1;0.724294,MA0088.1;0.20556,MA0089.1;0,MA0090.1;0.266215,MA0091.1;0.324543,MA0092.1;0.291716,MA0093.1;0.191154,MA0095.1;0,MA0098.1;0,MA0100.1;0.426863,MA0101.1;1.07376,MA0103.1;0.181541,MA0105.1;0.130274,MA0106.1;0.452066,MA0107.1;1.3641,MA0108.2;0.597764,MA0109.1;0,MA0111.1;0.761158,MA0113.1;0.467266,MA0114.1;0.134281,MA0115.1;0.992167,MA0116.1;0.854781,MA0117.1;0.792789,MA0119.1;1.20117,MA0122.1;0.818044,MA0124.1;0.951337,MA0125.1;0.868909,MA0130.1;0,MA0131.1;0.519055,MA0132.1;0,MA0133.1;0,MA0135.1;0.785738,MA0136.1;0.420617,MA0139.1;0.567946,MA0140.1;0.376643,MA0141.1;0.238287,MA0142.1;0.570448,MA0143.1;1.17969,MA0144.1;0.124153,MA0145.1;0.0932202,MA0146.1;0.0677137,MA0147.1;0.143012,MA0148.1;0.344198,MA0149.1;0.367947,MA0062.2;0.0823902,MA0035.2;0.376007,MA0039.2;1.23118,MA0138.2;0.503176,MA0002.2;0.316618,MA0137.2;0.20663,MA0104.2;0.102626,MA0047.2;0.440861,MA0112.2;0.416057,MA0065.2;0.23889,MA0150.1;0.261236,MA0151.1;0,MA0152.1;0.382565,MA0153.1;0.852412,MA0154.1;0.0310431,MA0155.1;0.202876,MA0156.1;0.208455,MA0157.1;0.544523,MA0158.1;0,MA0159.1;0.867657,MA0160.1;0.357736,MA0161.1;0,MA0162.1;1.19068,MA0163.1;4.60751,MA0164.1;0.478818,MA0080.2;0.191221,MA0018.2;1.14938,MA0099.2;0.382887,MA0079.2;11.3182,MA0102.2;1.28978,MA0258.1;0.117513,MA0259.1;0.455773,MA0442.1;0
}}
}}

Revision as of 19:23, 22 January 2013


Full id: C702_spinal_parietal_Neural_occipital_locus_temporal_globus



Phase1 CAGE Peaks

Hg19::chr15:93632421..93632446,-p1@RGMA
Hg19::chr16:72459838..72459857,+p1@uc002fch.1
Hg19::chr17:49124054..49124065,-p8@SPAG9
Hg19::chr17:54230819..54230848,+p1@ANKFN1
Hg19::chr19:51814892..51814930,+p1@IGLON5
Hg19::chr6:123154483..123154508,-p@chr6:123154483..123154508
-
Hg19::chr7:103969251..103969288,+p1@LHFPL3
Hg19::chr7:121513146..121513153,+p3@PTPRZ1
Hg19::chr7:121513171..121513202,+p2@PTPRZ1
Hg19::chr7:121513207..121513221,+p1@PTPRZ1
Hg19::chr8:63161180..63161204,+p4@NKAIN3
Hg19::chr8:85618155..85618173,+p3@RALYL


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:0001843neural tube closure0.0357467999751478
GO:0014020primary neural tube formation0.0357467999751478
GO:0001839neural plate morphogenesis0.0357467999751478
GO:0001841neural tube formation0.0357467999751478
GO:0001840neural plate development0.0357467999751478
GO:0001838embryonic epithelial tube formation0.0357467999751478
GO:0019198transmembrane receptor protein phosphatase activity0.0357467999751478
GO:0021915neural tube development0.0357467999751478
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0357467999751478
GO:0016331morphogenesis of embryonic epithelium0.0369304705862911
GO:0001669acrosome0.0369304705862911



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
neuronal stem cell1.69e-138
neuron4.85e-106
neuroblast4.85e-106
electrically signaling cell4.85e-106
neural cell2.35e-0925
embryonic stem cell1.90e-075
Uber Anatomy
Ontology termp-valuen
central nervous system8.91e-8981
neural tube4.67e-8856
neural rod4.67e-8856
future spinal cord4.67e-8856
neural keel4.67e-8856
nervous system6.81e-8389
regional part of nervous system1.78e-8253
regional part of brain1.78e-8253
brain8.27e-6868
future brain8.27e-6868
regional part of forebrain6.07e-6641
forebrain6.07e-6641
anterior neural tube6.07e-6641
future forebrain6.07e-6641
neural plate8.86e-6682
presumptive neural plate8.86e-6682
neurectoderm7.65e-6286
adult organism1.33e-61114
brain grey matter1.27e-5534
gray matter1.27e-5534
telencephalon4.23e-5534
cerebral hemisphere5.34e-5232
regional part of telencephalon6.24e-5232
ecto-epithelium1.84e-51104
pre-chordal neural plate9.22e-4761
ectoderm-derived structure5.31e-41171
ectoderm5.31e-41171
presumptive ectoderm5.31e-41171
cerebral cortex3.28e-4025
pallium3.28e-4025
organ system subdivision3.76e-40223
structure with developmental contribution from neural crest4.94e-38132
regional part of cerebral cortex8.72e-3622
neocortex3.00e-3220
posterior neural tube4.80e-2215
chordal neural plate4.80e-2215
anatomical cluster3.08e-21373
tube8.70e-21192
segmental subdivision of nervous system2.15e-1813
segmental subdivision of hindbrain5.93e-1712
hindbrain5.93e-1712
presumptive hindbrain5.93e-1712
neural nucleus1.41e-169
nucleus of brain1.41e-169
basal ganglion1.98e-169
nuclear complex of neuraxis1.98e-169
aggregate regional part of brain1.98e-169
collection of basal ganglia1.98e-169
cerebral subcortex1.98e-169
anatomical conduit1.09e-15240
organ part3.60e-13218
telencephalic nucleus5.07e-137
embryo1.39e-12592
multi-tissue structure1.68e-12342
regional part of metencephalon5.52e-129
metencephalon5.52e-129
future metencephalon5.52e-129
diencephalon6.42e-127
future diencephalon6.42e-127
brainstem8.72e-126
gyrus2.71e-116
germ layer2.71e-10560
germ layer / neural crest2.71e-10560
embryonic tissue2.71e-10560
presumptive structure2.71e-10560
germ layer / neural crest derived structure2.71e-10560
epiblast (generic)2.71e-10560
limbic system3.69e-105
epithelium3.73e-10306
embryonic structure4.95e-10564
occipital lobe5.52e-105
cell layer6.93e-10309
temporal lobe9.15e-106
parietal lobe1.42e-095
developing anatomical structure1.90e-09581
organ3.17e-09503
multi-cellular organism4.48e-09656
corpus striatum3.72e-084
striatum3.72e-084
ventral part of telencephalon3.72e-084
future corpus striatum3.72e-084
regional part of diencephalon9.86e-084
anatomical system1.87e-07624
anatomical group2.12e-07625
cerebellum3.73e-076
rhombic lip3.73e-076
gland of diencephalon6.11e-074
neuroendocrine gland6.11e-074
spinal cord8.26e-073
dorsal region element8.26e-073
dorsum8.26e-073
medulla oblongata9.77e-073
myelencephalon9.77e-073
future myelencephalon9.77e-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)
MA0003.10.881315
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.12.20911
MA0017.10.627635
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.641892
MA0050.10.837296
MA0051.10.410316
MA0052.10.682867
MA0055.10.901232
MA0056.10
MA0057.11.38004
MA0058.10.240796
MA0059.10.239727
MA0060.10.337131
MA0061.10.28989
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.226673
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.17.64865
MA0074.10.40963
MA0076.10.254045
MA0077.11.70983
MA0078.11.25378
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.20556
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.11.07376
MA0103.10.181541
MA0105.10.130274
MA0106.10.452066
MA0107.11.3641
MA0108.20.597764
MA0109.10
MA0111.10.761158
MA0113.10.467266
MA0114.10.134281
MA0115.10.992167
MA0116.10.854781
MA0117.10.792789
MA0119.11.20117
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.567946
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.11.17969
MA0144.10.124153
MA0145.10.0932202
MA0146.10.0677137
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.21.23118
MA0138.20.503176
MA0002.20.316618
MA0137.20.20663
MA0104.20.102626
MA0047.20.440861
MA0112.20.416057
MA0065.20.23889
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.0310431
MA0155.10.202876
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.867657
MA0160.10.357736
MA0161.10
MA0162.11.19068
MA0163.14.60751
MA0164.10.478818
MA0080.20.191221
MA0018.21.14938
MA0099.20.382887
MA0079.211.3182
MA0102.21.28978
MA0258.10.117513
MA0259.10.455773
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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C702&oldid=2569213"