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Coexpression cluster:C735: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.704765,0.306045,1.27852,0.975357,0.21227,0.371921,0.44126,0.121034,0.379568,0.185549,0.344881,0.481459,0.628958,0.430675,0.211157,0.651838,0.650562,0.504019,0.0986515,0.339956,0.246975,0.0198455,0.36495,0.20812,0.779948,0.50266,0.267398,0.363006,0.214796,0.517293,0.325512,0.685875,0.869588,0.307151,0.184525,2.86872,1.02692,0.372963,0.163827,1.16543,0.183426,1.51389,0.250399,0.209923,0.0277665,0.273032,0.442265,0.89086,0.437532,0.615345,0.515974,0.453148,0.179579,0.760015,0.908824,0.433372,0.623552,0.40339,0.0681812,0.402472,0.725346,0.444449,0.763639,1.51165,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.299692,0.787952,0.702612,0.906867,0.29535,0.273699,0.071925,0.607953,0.672773,0.767864,2.26324,0.623044,0.46072,0.778826,0.856604,0.107378,0.144665,1.30398,0.540459,1.45821,1.08742,0.830286,0.702047,0.892354,0.212875,1.49285,0.322542,0.743159,0.544807,0.207288,0.957175,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.779451,0.199366,0.712243,0.735091,0.679564,0.353283,1.04009,0.533593,0.47353,0.324453,0.58906,0.461431,0.898765,0.538171,0.369441,0.471181,1.14929,1.47938,0.435413,0.706859,0.940494,0.159968,0.830959,0.328039,0.954592,0.468088,1.10012,1.26269,1.54623,0.953561,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,0.395692,0.566218,1.75262,0.308276,0.146851,0.160217,0.234905,0.831331,0.737254,0.444001,1.22899,0.525224,0.582239,0.780063,0.261307,1.02032,0.813307,0.672017,0.264042,0.597299,0.459987,0.843711,0.440034,0.452975
|tfbs_overrepresentation_for_novel_motifs=0.704765,0.306045,1.27852,0.975357,0.21227,0.371921,0.44126,0.121034,0.379568,0.185549,0.344881,0.481459,0.628958,0.430675,0.211157,0.651838,0.650562,0.504019,0.0986515,0.339956,0.246975,0.0198455,0.36495,0.20812,0.779948,0.50266,0.267398,0.363006,0.214796,0.517293,0.325512,0.685875,0.869588,0.307151,0.184525,2.86872,1.02692,0.372963,0.163827,1.16543,0.183426,1.51389,0.250399,0.209923,0.0277665,0.273032,0.442265,0.89086,0.437532,0.615345,0.515974,0.453148,0.179579,0.760015,0.908824,0.433372,0.623552,0.40339,0.0681812,0.402472,0.725346,0.444449,0.763639,1.51165,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.299692,0.787952,0.702612,0.906867,0.29535,0.273699,0.071925,0.607953,0.672773,0.767864,2.26324,0.623044,0.46072,0.778826,0.856604,0.107378,0.144665,1.30398,0.540459,1.45821,1.08742,0.830286,0.702047,0.892354,0.212875,1.49285,0.322542,0.743159,0.544807,0.207288,0.957175,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.779451,0.199366,0.712243,0.735091,0.679564,0.353283,1.04009,0.533593,0.47353,0.324453,0.58906,0.461431,0.898765,0.538171,0.369441,0.471181,1.14929,1.47938,0.435413,0.706859,0.940494,0.159968,0.830959,0.328039,0.954592,0.468088,1.10012,1.26269,1.54623,0.953561,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,0.395692,0.566218,1.75262,0.308276,0.146851,0.160217,0.234905,0.831331,0.737254,0.444001,1.22899,0.525224,0.582239,0.780063,0.261307,1.02032,0.813307,0.672017,0.264042,0.597299,0.459987,0.843711,0.440034,0.452975
|tfbs_overrepresentation_jaspar=MA0003.1;0.0370565,MA0004.1;0.349539,MA0006.1;0.210781,MA0007.1;0.332734,MA0009.1;0.79061,MA0014.1;0.0481212,MA0017.1;0.24363,MA0019.1;0.486183,MA0024.1;0.688373,MA0025.1;0.921763,MA0027.1;2.39404,MA0028.1;0.224112,MA0029.1;0.707146,MA0030.1;0.696006,MA0031.1;0.633489,MA0038.1;0.443833,MA0040.1;0.712837,MA0041.1;0.366339,MA0042.1;0.337481,MA0043.1;0.790919,MA0046.1;0.779945,MA0048.1;1.12059,MA0050.1;0.338274,MA0051.1;0.439895,MA0052.1;0.716602,MA0055.1;1.40057,MA0056.1;0,MA0057.1;0.703296,MA0058.1;0.265212,MA0059.1;0.2641,MA0060.1;0.119532,MA0061.1;0.100525,MA0063.1;0,MA0066.1;0.444231,MA0067.1;1.1037,MA0068.1;1.95025,MA0069.1;0.776171,MA0070.1;0.765217,MA0071.1;0.40788,MA0072.1;0.760818,MA0073.1;3.00767,MA0074.1;0.439193,MA0076.1;0.278993,MA0077.1;0.753278,MA0078.1;1.32052,MA0081.1;0.26424,MA0083.1;0.79797,MA0084.1;1.28962,MA0087.1;0.758426,MA0088.1;0.467716,MA0089.1;0,MA0090.1;0.291627,MA0091.1;0.351901,MA0092.1;0.318032,MA0093.1;0.213288,MA0095.1;0,MA0098.1;0,MA0100.1;0.456802,MA0101.1;0.216017,MA0103.1;0.587485,MA0105.1;0.15707,MA0106.1;0.482519,MA0107.1;0.475157,MA0108.2;0.630531,MA0109.1;0,MA0111.1;0.303543,MA0113.1;0.498009,MA0114.1;0.153042,MA0115.1;1.02805,MA0116.1;0.159642,MA0117.1;0.827487,MA0119.1;0.250314,MA0122.1;0.852927,MA0124.1;0.98702,MA0125.1;0.904129,MA0130.1;0,MA0131.1;0.550695,MA0132.1;0,MA0133.1;0,MA0135.1;0.820382,MA0136.1;0.450422,MA0139.1;0.307853,MA0140.1;0.405425,MA0141.1;0.2626,MA0142.1;0.602852,MA0143.1;0.498176,MA0144.1;0.142196,MA0145.1;0.277793,MA0146.1;0.0109959,MA0147.1;0.162359,MA0148.1;0.372124,MA0149.1;0.396509,MA0062.2;0.0969238,MA0035.2;0.404774,MA0039.2;0.166893,MA0138.2;0.534556,MA0002.2;0.111226,MA0137.2;0.229531,MA0104.2;0.378829,MA0047.2;0.47109,MA0112.2;0.106997,MA0065.2;0.11899,MA0150.1;0.286461,MA0151.1;0,MA0152.1;0.411494,MA0153.1;0.887528,MA0154.1;1.41082,MA0155.1;0.74825,MA0156.1;0.231442,MA0157.1;0.576556,MA0158.1;0,MA0159.1;0.489747,MA0160.1;0.386031,MA0161.1;0,MA0162.1;0.519336,MA0163.1;0.232847,MA0164.1;1.2703,MA0080.2;0.21336,MA0018.2;0.483823,MA0099.2;0.411824,MA0079.2;2.64424,MA0102.2;1.32663,MA0258.1;0.135061,MA0259.1;0.504687,MA0442.1;0
}}
}}

Revision as of 19:24, 22 January 2013


Full id: C735_hippocampus_medial_olfactory_amygdala_occipital_insula_middle



Phase1 CAGE Peaks

Hg19::chr11:133197324..133197336,-p@chr11:133197324..133197336
-
Hg19::chr11:94134180..94134196,-p1@AB384231
Hg19::chr11:94134299..94134309,-p2@AB384231
Hg19::chr12:118406198..118406208,-p17@KSR2
Hg19::chr12:41221619..41221633,+p7@CNTN1
Hg19::chr19:18309621..18309636,-p@chr19:18309621..18309636
-
Hg19::chr19:47763015..47763035,+p@chr19:47763015..47763035
+
Hg19::chr19:54462405..54462474,+p@chr19:54462405..54462474
+
Hg19::chr22:18592469..18592498,+p@chr22:18592469..18592498
+
Hg19::chr8:144241413..144241426,-p3@LY6H
Hg19::chr9:13165441..13165450,-p20@MPDZ


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:0008289lipid binding0.00157559168692717
GO:0048503GPI anchor binding0.00330020851256108
GO:0035091phosphoinositide binding0.00872259388036306
GO:0005543phospholipid binding0.0115574480250189
GO:0005624membrane fraction0.0381913489365482
GO:0000267cell fraction0.048973045288048
GO:0019717synaptosome0.048973045288048



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
neural tube7.70e-10256
neural rod7.70e-10256
future spinal cord7.70e-10256
neural keel7.70e-10256
regional part of nervous system1.17e-10153
regional part of brain1.17e-10153
brain6.60e-8768
future brain6.60e-8768
telencephalon1.36e-8634
brain grey matter3.83e-8634
gray matter3.83e-8634
cerebral hemisphere5.28e-8532
regional part of forebrain2.07e-8341
forebrain2.07e-8341
anterior neural tube2.07e-8341
future forebrain2.07e-8341
central nervous system3.99e-8181
regional part of telencephalon9.40e-7832
nervous system1.63e-7289
regional part of cerebral cortex9.50e-7022
neural plate7.94e-6882
presumptive neural plate7.94e-6882
neurectoderm2.14e-6486
cerebral cortex3.19e-6125
pallium3.19e-6125
neocortex2.21e-6020
adult organism3.70e-57114
pre-chordal neural plate1.35e-5461
ecto-epithelium3.46e-52104
structure with developmental contribution from neural crest1.73e-42132
ectoderm-derived structure4.90e-35171
ectoderm4.90e-35171
presumptive ectoderm4.90e-35171
gyrus9.51e-326
organ system subdivision6.01e-27223
basal ganglion1.46e-269
nuclear complex of neuraxis1.46e-269
aggregate regional part of brain1.46e-269
collection of basal ganglia1.46e-269
cerebral subcortex1.46e-269
limbic system7.90e-265
neural nucleus9.25e-269
nucleus of brain9.25e-269
tube3.10e-25192
corpus striatum2.91e-204
striatum2.91e-204
ventral part of telencephalon2.91e-204
future corpus striatum2.91e-204
brainstem1.48e-196
posterior neural tube3.56e-1915
chordal neural plate3.56e-1915
temporal lobe6.66e-196
anatomical conduit8.28e-19240
segmental subdivision of hindbrain1.26e-1812
hindbrain1.26e-1812
presumptive hindbrain1.26e-1812
telencephalic nucleus1.42e-177
parietal lobe3.65e-175
segmental subdivision of nervous system3.95e-1713
frontal cortex1.28e-163
organ part8.71e-16218
caudate-putamen1.28e-153
dorsal striatum1.28e-153
pons6.61e-153
anatomical cluster2.60e-13373
epithelium3.07e-13306
regional part of metencephalon3.21e-139
metencephalon3.21e-139
future metencephalon3.21e-139
cell layer4.83e-13309
middle frontal gyrus6.27e-122
middle temporal gyrus7.35e-122
amygdala1.70e-112
Ammon's horn1.89e-112
lobe parts of cerebral cortex1.89e-112
hippocampal formation1.89e-112
limbic lobe1.89e-112
multi-tissue structure4.18e-11342
caudate nucleus5.00e-112
future caudate nucleus5.00e-112
dorsal plus ventral thalamus6.13e-112
thalamic complex6.13e-112
locus ceruleus1.93e-102
brainstem nucleus1.93e-102
hindbrain nucleus1.93e-102
occipital lobe1.12e-095
organ3.52e-07503
medulla oblongata3.58e-073
myelencephalon3.58e-073
future myelencephalon3.58e-073
olfactory region9.81e-071
primary subdivision of skull9.81e-071
cranium9.81e-071
neurocranium9.81e-071
chondrocranium9.81e-071
cartilaginous neurocranium9.81e-071
head paraxial mesoderm9.81e-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)
MA0003.10.0370565
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.0481212
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.11.12059
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.11.40057
MA0056.10
MA0057.10.703296
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.11.95025
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.13.00767
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.11.32052
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.467716
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.10.15707
MA0106.10.482519
MA0107.10.475157
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.307853
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.277793
MA0146.10.0109959
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.166893
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.378829
MA0047.20.47109
MA0112.20.106997
MA0065.20.11899
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.11.41082
MA0155.10.74825
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.10.386031
MA0161.10
MA0162.10.519336
MA0163.10.232847
MA0164.11.2703
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.22.64424
MA0102.21.32663
MA0258.10.135061
MA0259.10.504687
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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