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Coexpression cluster:C1014: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.64689,0.183537,2.45456,0.481684,0.301904,0.480078,0.554663,0.19223,0.190005,4.29816,1.99636,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.560708,0.341703,0.405031,1.1906,0.29709,0.385586,0.619829,0.421276,0.470396,0.822672,0.777139,0.429397,0.810962,0.220667,0.154814,0.269459,0.339976,0.735464,0.481208,0.244807,0.174436,0.268162,2.79631,0.201367,0.809926,3.23731,0.371118,0.555735,1.12076,0.186577,0.304949,0.63387,0.567337,0.639783,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,1.76725,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,2.13929,1.03748,2.05941,0.138565,0.401476,0.730167,0.797419,0.379656,1.54232,1.76505,0.575394,0.19474,0.986227,7.65042,0.26222,0.118789,1.58596,1.59442,1.22073,0.959334,0.827657,0.227232,1.48306,0.672575,0.162291,0.87,0.664183,0.345507,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,1.77423,1.42617,0.352381,0.861701,0.893372,0.459808,1.17281,0.265019,2.10876,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.364369,0.423593,0.470947,1.19123,2.04907,1.64679,2.59859,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.637373,0.999704,2.1277,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,1.00225,2.53311,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.664626
|tfbs_overrepresentation_jaspar=MA0003.1;3.70381,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;2.6969,MA0017.1;0.896777,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.846854,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;1.95652,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.653157,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.524515,MA0056.1;0,MA0057.1;1.05663,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.497495,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.415214,MA0069.1;2.08998,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.0136601,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.054222,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.279181,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.655057,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;2.71361,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;1.46857,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;1.7555,MA0146.1;0.239099,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.485915,MA0035.2;0.515566,MA0039.2;0.44475,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.55506,MA0047.2;1.43258,MA0112.2;0.0572179,MA0065.2;1.27835,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.274121,MA0155.1;0.197713,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;3.77262,MA0163.1;0.288263,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;6.80121,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0
}}
}}

Revision as of 19:37, 22 January 2013


Full id: C1014_hippocampus_locus_spinal_medulla_neuroectodermal_cerebellum_thalamus



Phase1 CAGE Peaks

Hg19::chr12:41221634..41221645,+p15@CNTN1
Hg19::chr12:41221646..41221663,+p10@CNTN1
Hg19::chr17:11143523..11143550,+p@chr17:11143523..11143550
+
Hg19::chr17:11143564..11143575,+p@chr17:11143564..11143575
+
Hg19::chr17:11143854..11143894,+p@chr17:11143854..11143894
+
Hg19::chr17:11143968..11143990,+p@chr17:11143968..11143990
+
Hg19::chr17:11144505..11144535,+p1@SHISA6
Hg19::chr17:11144580..11144595,+p2@SHISA6


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:0007219Notch signaling pathway0.0235488048981514
GO:0048503GPI anchor binding0.0296714941716708
GO:0035091phosphoinositide binding0.0393265041799129
GO:0005543phospholipid binding0.0393265041799129



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 cell2.95e-095
Uber Anatomy
Ontology termp-valuen
neural tube1.92e-6456
neural rod1.92e-6456
future spinal cord1.92e-6456
neural keel1.92e-6456
central nervous system1.20e-6081
nervous system3.32e-5889
regional part of nervous system4.43e-5853
regional part of brain4.43e-5853
adult organism6.21e-56114
brain8.06e-4768
future brain8.06e-4768
brain grey matter5.84e-4434
gray matter5.84e-4434
neurectoderm7.21e-4486
regional part of forebrain1.73e-4341
forebrain1.73e-4341
anterior neural tube1.73e-4341
future forebrain1.73e-4341
telencephalon1.84e-4334
neural plate5.13e-4282
presumptive neural plate5.13e-4282
cerebral hemisphere6.06e-4032
regional part of telencephalon9.87e-4032
regional part of cerebral cortex2.55e-3922
neocortex6.56e-3520
cerebral cortex5.19e-3425
pallium5.19e-3425
ecto-epithelium4.74e-32104
ectoderm-derived structure1.70e-29171
ectoderm1.70e-29171
presumptive ectoderm1.70e-29171
pre-chordal neural plate3.43e-2861
structure with developmental contribution from neural crest3.13e-26132
organ system subdivision2.49e-23223
posterior neural tube1.49e-2115
chordal neural plate1.49e-2115
segmental subdivision of hindbrain2.38e-1512
hindbrain2.38e-1512
presumptive hindbrain2.38e-1512
brainstem9.53e-156
segmental subdivision of nervous system5.35e-1413
gyrus1.14e-136
anatomical cluster1.43e-12373
tube2.03e-12192
limbic system3.44e-125
temporal lobe1.27e-116
parietal lobe2.39e-115
neural nucleus2.92e-119
nucleus of brain2.92e-119
basal ganglion4.02e-119
nuclear complex of neuraxis4.02e-119
aggregate regional part of brain4.02e-119
collection of basal ganglia4.02e-119
cerebral subcortex4.02e-119
anatomical conduit1.59e-10240
embryo9.06e-10592
regional part of metencephalon1.71e-099
metencephalon1.71e-099
future metencephalon1.71e-099
spinal cord2.84e-083
dorsal region element2.84e-083
dorsum2.84e-083
pons2.90e-083
medulla oblongata3.66e-083
myelencephalon3.66e-083
future myelencephalon3.66e-083
epithelium5.06e-08306
organ part7.26e-08218
cell layer8.09e-08309
frontal cortex9.69e-083
multi-cellular organism1.06e-07656
occipital lobe1.95e-075
telencephalic nucleus2.42e-077
multi-tissue structure2.52e-07342
male genital duct6.89e-073
internal male genitalia6.89e-073
developing anatomical structure9.58e-07581


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)
MA0003.13.70381
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.12.6969
MA0017.10.896777
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.11.95652
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.524515
MA0056.10
MA0057.11.05663
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.12.08998
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0136601
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.12.71361
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.11.46857
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.11.7555
MA0146.10.239099
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.20.44475
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.55506
MA0047.21.43258
MA0112.20.0572179
MA0065.21.27835
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.13.77262
MA0163.10.288263
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.26.80121
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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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