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{{Coexpression_clusters
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80698,0.267192,0.0559205,0.215792,0.379171,0.214946,0.333105,0.222472,0.252354,0.396678,0.00926835,0.152456,0.224382,0.0472558,0.128266,0.412357,0.567591,0.723546,0.129023,0.462987,0.429017,0.308191,0.295133,0.558985,0.244535,0.142722,0.657687,0.511893,0.705698,0.104872,0.404324,0.473851,0.571258,0.196505,0.12925,0.0783346,0.0585708,0.363221,0.000347274,0.605083,0.361802,0.189507,0.540283,0.123414,0.344927,0.651673,0.482941,0.605877,0.302498,0.0165552,0.608655,0.574325,0.30896,0.280668,0.0534139,0.498751,0.133309,0.00676098,0.236983,0.685564,0.323272,0.602683,0.00602793,0.466029,0.589709,0.0933285,0.0541993,0.806913|tfbs_overrepresentation_for_novel_motifs=0.253158,0.727456,0.246925,0.373402,0.21227,0.972097,0.44126,0.769964,0.379568,0.905388,0.344881,0.481459,0.3032,0.430675,0.211157,0.230406,0.650562,0.168654,1.10831,0.339956,0.246975,0.0880531,0.36495,0.20812,0.779948,0.50266,0.267398,0.363006,0.214796,0.24094,0.325512,0.685875,0.869588,0.635939,0.184525,4.95374,0.536602,0.372963,0.163827,2.32223,0.183426,0.836994,0.471149,0.209923,0.183826,0.273032,0.442265,0.335245,1.43924,0.615345,0.515974,0.453148,0.712499,0.760015,0.908824,0.433372,0.623552,0.40339,0.516954,0.402472,0.725346,0.444449,0.380466,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.299692,0.394628,1.08398,0.906867,0.615054,0.576459,0.071925,0.607953,0.672773,0.280653,0.101808,0.623044,0.46072,0.123028,0.856604,0.400752,0.0364455,2.38283,0.540459,1.45821,1.08742,0.830286,0.702047,0.149302,0.610551,0.480816,0.322542,0.743159,0.544807,0.455381,0.957175,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.578396,0.256397,0.735091,0.242288,0.353283,1.04009,0.533593,0.47353,0.324453,0.58906,0.151445,0.898765,0.538171,0.966635,0.471181,1.14929,0.608677,0.435413,0.706859,0.940494,0.159968,0.830959,0.328039,0.954592,1.18111,1.10012,2.31893,2.35002,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,0.395692,0.566218,1.75262,0.830443,0.449933,0.655201,0.723917,0.831331,0.737254,0.444001,1.22899,0.525224,0.200973,0.286011,0.261307,1.02032,0.813307,0.672017,0.264042,0.597299,0.459987,0.137885,1.12065,0.183548|tfbs_overrepresentation_jaspar=MA0003.1;0.0768054,MA0004.1;0.349539,MA0006.1;0.605586,MA0007.1;0.332734,MA0009.1;0.79061,MA0014.1;0.36818,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;0.729247,MA0050.1;0.338274,MA0051.1;0.439895,MA0052.1;0.716602,MA0055.1;1.40057,MA0056.1;0,MA0057.1;2.60171,MA0058.1;0.265212,MA0059.1;0.2641,MA0060.1;0.38025,MA0061.1;0.100525,MA0063.1;0,MA0066.1;0.444231,MA0067.1;1.1037,MA0068.1;0.262497,MA0069.1;0.776171,MA0070.1;0.765217,MA0071.1;0.40788,MA0072.1;0.760818,MA0073.1;0.417932,MA0074.1;0.439193,MA0076.1;0.278993,MA0077.1;0.753278,MA0078.1;0.533387,MA0081.1;0.26424,MA0083.1;1.87258,MA0084.1;1.28962,MA0087.1;0.758426,MA0088.1;0.467716,MA0089.1;0,MA0090.1;0.291627,MA0091.1;0.927876,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;0.156959,MA0108.2;0.630531,MA0109.1;0,MA0111.1;1.48644,MA0113.1;0.498009,MA0114.1;0.465415,MA0115.1;1.02805,MA0116.1;0.481808,MA0117.1;0.827487,MA0119.1;0.698186,MA0122.1;0.852927,MA0124.1;0.98702,MA0125.1;0.904129,MA0130.1;0,MA0131.1;2.32762,MA0132.1;0,MA0133.1;0,MA0135.1;0.820382,MA0136.1;0.450422,MA0139.1;0.307853,MA0140.1;0.405425,MA0141.1;0.726533,MA0142.1;0.602852,MA0143.1;0.498176,MA0144.1;0.862195,MA0145.1;0.115359,MA0146.1;0.184736,MA0147.1;0.488526,MA0148.1;0.372124,MA0149.1;0.396509,MA0062.2;0.0969238,MA0035.2;0.404774,MA0039.2;0.556508,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;0.839576,MA0150.1;0.286461,MA0151.1;0,MA0152.1;0.411494,MA0153.1;0.887528,MA0154.1;0.153348,MA0155.1;0.462858,MA0156.1;0.231442,MA0157.1;0.576556,MA0158.1;0,MA0159.1;0.162854,MA0160.1;0.386031,MA0161.1;0,MA0162.1;0.0266618,MA0163.1;0.387319,MA0164.1;0.509774,MA0080.2;0.21336,MA0018.2;0.483823,MA0099.2;0.411824,MA0079.2;2.90119,MA0102.2;1.32663,MA0258.1;0.420151,MA0259.1;0.168926,MA0442.1;0}}
|full_id=C755_cerebellum_parietal_temporal_occipital_duodenum_brain_hippocampus
|id=C755
}}

Latest revision as of 11:30, 17 September 2013


Full id: C755_cerebellum_parietal_temporal_occipital_duodenum_brain_hippocampus



Phase1 CAGE Peaks

Hg19::chr14:23982181..23982193,-p@chr14:23982181..23982193
-
Hg19::chr17:2679600..2679618,+p@chr17:2679600..2679618
+
Hg19::chr19:42817494..42817510,+p5@TMEM145
Hg19::chr1:42384322..42384336,-p5@HIVEP3
Hg19::chr5:87979375..87979388,-p@chr5:87979375..87979388
-
Hg19::chr5:87980660..87980676,-p8@LINC00461
Hg19::chr5:87980761..87980821,-p4@LINC00461
Hg19::chr7:82753269..82753271,-p@chr7:82753269..82753271
-
Hg19::chr8:10192782..10192787,+p@chr8:10192782..10192787
+
Hg19::chr8:85114625..85114629,+p@chr8:85114625..85114629
+
Hg19::chr8:9970823..9970828,+p@chr8:9970823..9970828
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube4.62e-10956
neural rod4.62e-10956
future spinal cord4.62e-10956
neural keel4.62e-10956
regional part of nervous system1.00e-10453
regional part of brain1.00e-10453
central nervous system8.47e-9181
brain4.36e-8768
future brain4.36e-8768
regional part of forebrain4.78e-8741
forebrain4.78e-8741
anterior neural tube4.78e-8741
future forebrain4.78e-8741
nervous system1.98e-8489
telencephalon8.83e-8234
brain grey matter1.27e-8134
gray matter1.27e-8134
cerebral hemisphere1.42e-7532
neural plate2.95e-7582
presumptive neural plate2.95e-7582
regional part of telencephalon3.09e-7532
neurectoderm9.95e-7586
ecto-epithelium3.64e-60104
pre-chordal neural plate8.55e-6061
cerebral cortex2.71e-5825
pallium2.71e-5825
regional part of cerebral cortex5.41e-5522
neocortex3.17e-5420
structure with developmental contribution from neural crest9.71e-48132
ectoderm-derived structure2.24e-45171
ectoderm2.24e-45171
presumptive ectoderm2.24e-45171
adult organism1.04e-43114
organ system subdivision1.71e-32223
tube1.77e-26192
basal ganglion7.52e-259
nuclear complex of neuraxis7.52e-259
aggregate regional part of brain7.52e-259
collection of basal ganglia7.52e-259
cerebral subcortex7.52e-259
neural nucleus3.30e-249
nucleus of brain3.30e-249
posterior neural tube3.35e-2215
chordal neural plate3.35e-2215
brainstem1.03e-206
temporal lobe3.60e-196
anatomical conduit3.69e-19240
parietal lobe5.06e-195
segmental subdivision of hindbrain3.27e-1812
hindbrain3.27e-1812
presumptive hindbrain3.27e-1812
telencephalic nucleus5.07e-187
segmental subdivision of nervous system1.05e-1613
anatomical cluster5.12e-16373
gyrus1.08e-156
organ part5.36e-15218
epithelium1.25e-14306
cell layer2.18e-14309
limbic system2.15e-125
occipital lobe2.34e-125
medulla oblongata2.27e-113
myelencephalon2.27e-113
future myelencephalon2.27e-113
multi-tissue structure3.07e-11342
pons4.44e-113
regional part of metencephalon4.60e-109
metencephalon4.60e-109
future metencephalon4.60e-109
corpus striatum7.25e-094
striatum7.25e-094
ventral part of telencephalon7.25e-094
future corpus striatum7.25e-094
amygdala9.93e-092
middle temporal gyrus1.24e-082
globus pallidus3.60e-082
pallidum3.60e-082
germ layer4.35e-08560
germ layer / neural crest4.35e-08560
embryonic tissue4.35e-08560
presumptive structure4.35e-08560
germ layer / neural crest derived structure4.35e-08560
epiblast (generic)4.35e-08560
diencephalon5.24e-087
future diencephalon5.24e-087
locus ceruleus5.54e-082
brainstem nucleus5.54e-082
hindbrain nucleus5.54e-082
embryonic structure6.00e-08564
organ1.31e-07503
meninx1.82e-072
membrane organ1.82e-072
meningeal cluster1.82e-072
developing anatomical structure2.26e-07581
embryo5.11e-07592


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)
MA0003.10.0768054
MA0004.10.349539
MA0006.10.605586
MA0007.10.332734
MA0009.10.79061
MA0014.10.36818
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
MA0048.10.729247
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.11.40057
MA0056.10
MA0057.12.60171
MA0058.10.265212
MA0059.10.2641
MA0060.10.38025
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.262497
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.417932
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.11.87258
MA0084.11.28962
MA0087.10.758426
MA0088.10.467716
MA0089.10
MA0090.10.291627
MA0091.10.927876
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
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.11.48644
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.481808
MA0117.10.827487
MA0119.10.698186
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.12.32762
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.307853
MA0140.10.405425
MA0141.10.726533
MA0142.10.602852
MA0143.10.498176
MA0144.10.862195
MA0145.10.115359
MA0146.10.184736
MA0147.10.488526
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.556508
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.378829
MA0047.20.47109
MA0112.20.106997
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.153348
MA0155.10.462858
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.0266618
MA0163.10.387319
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.22.90119
MA0102.21.32663
MA0258.10.420151
MA0259.10.168926
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
CTBP2#1488317.10463645618040.0006070928651993480.00506787401075491



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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