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Coexpression cluster:C1247: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.0232809,0.384703,0.529489,0.343148,0.52784,0.604235,0.643217,0.224331,0.200685,0.497563,1.5614,0.184039,0.592674,0.341795,0.365029,0.827563,0.28906,0.19568,0.0986842,0.384762,0.0646572,0.520063,0.338096,0.430372,1.60904,0.49486,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.232776,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,0.254304,0.340293,0.265117,0.415364,0.60533,0.486696,0.511111,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.656075,0.115253,1.0929,0.179863,0.168304,0.473656,0.782748,0.850825,0.424224,0.580264,0.798651,0.625403,0.649554,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.73028,0.343884,1.39025,0.566252,0.924148,0.715799,0.413337,0.776034,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.988112,0.507004,1.22894,0.304323,0.039977,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,2.06018,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,1.15519,0.26104,0.106334,0.0685123,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.00626991
|tfbs_overrepresentation_jaspar=MA0003.1;0.00215847,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0156227,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;1.22641,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.120314,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;1.04727,MA0059.1;0.404929,MA0060.1;0.638423,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.488375,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.0282921,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;0.0723293,MA0089.1;0,MA0090.1;0.436918,MA0091.1;2.179,MA0092.1;0.467172,MA0093.1;0.9112,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,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;2.64084,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;0.0807715,MA0146.1;0.0127148,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.00276064,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.262665,MA0065.2;0.0828768,MA0150.1;1.10099,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,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;0.106355,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.911393,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;1.2885e-05,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:48, 22 January 2013


Full id: C1247_parietal_thalamus_hippocampus_olfactory_middle_amygdala_medial



Phase1 CAGE Peaks

Hg19::chr1:14819044..14819065,+p@chr1:14819044..14819065
+
Hg19::chr2:210526133..210526141,+p52@MAP2
Hg19::chr3:10369338..10369362,-p@chr3:10369338..10369362
-
Hg19::chr5:58148556..58148559,+p@chr5:58148556..58148559
+
Hg19::chr5:71502197..71502220,+p@chr5:71502197..71502220
+
Hg19::chr8:91969565..91969587,+p@chr8:91969565..91969587
+
Hg19::chr8:91969795..91969807,+p@chr8:91969795..91969807
+


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 tube3.92e-13656
neural rod3.92e-13656
future spinal cord3.92e-13656
neural keel3.92e-13656
regional part of nervous system1.18e-12453
regional part of brain1.18e-12453
brain grey matter9.50e-10734
gray matter9.50e-10734
telencephalon5.58e-10634
regional part of forebrain1.15e-10541
forebrain1.15e-10541
anterior neural tube1.15e-10541
future forebrain1.15e-10541
central nervous system1.02e-9981
brain4.44e-9968
future brain4.44e-9968
cerebral hemisphere5.24e-9932
regional part of telencephalon5.85e-9932
neural plate1.23e-9082
presumptive neural plate1.23e-9082
nervous system4.66e-8989
neurectoderm4.78e-8686
regional part of cerebral cortex1.77e-8222
neocortex1.72e-7420
cerebral cortex2.57e-7225
pallium2.57e-7225
ecto-epithelium1.01e-69104
pre-chordal neural plate5.37e-6961
adult organism2.36e-60114
structure with developmental contribution from neural crest5.48e-56132
ectoderm-derived structure1.10e-42171
ectoderm1.10e-42171
presumptive ectoderm1.10e-42171
basal ganglion6.26e-369
nuclear complex of neuraxis6.26e-369
aggregate regional part of brain6.26e-369
collection of basal ganglia6.26e-369
cerebral subcortex6.26e-369
tube1.75e-35192
neural nucleus2.05e-359
nucleus of brain2.05e-359
organ system subdivision5.39e-34223
posterior neural tube9.66e-3015
chordal neural plate9.66e-3015
telencephalic nucleus7.20e-287
anatomical conduit1.56e-26240
gyrus1.05e-246
brainstem2.57e-236
temporal lobe2.39e-216
limbic system5.84e-215
parietal lobe1.22e-205
occipital lobe1.44e-205
segmental subdivision of hindbrain1.02e-1912
hindbrain1.02e-1912
presumptive hindbrain1.02e-1912
epithelium8.90e-19306
cell layer1.67e-18309
organ part1.92e-18218
segmental subdivision of nervous system4.20e-1813
anatomical cluster1.20e-17373
corpus striatum3.83e-174
striatum3.83e-174
ventral part of telencephalon3.83e-174
future corpus striatum3.83e-174
multi-tissue structure9.80e-15342
caudate-putamen8.54e-143
dorsal striatum8.54e-143
frontal cortex2.44e-133
spinal cord6.81e-133
dorsal region element6.81e-133
dorsum6.81e-133
pons8.02e-133
medulla oblongata3.01e-123
myelencephalon3.01e-123
future myelencephalon3.01e-123
regional part of metencephalon7.76e-119
metencephalon7.76e-119
future metencephalon7.76e-119
middle frontal gyrus8.13e-102
amygdala8.48e-102
middle temporal gyrus8.85e-102
organ9.70e-10503
caudate nucleus1.05e-092
future caudate nucleus1.05e-092
Ammon's horn1.54e-092
lobe parts of cerebral cortex1.54e-092
hippocampal formation1.54e-092
limbic lobe1.54e-092
dorsal plus ventral thalamus2.75e-092
thalamic complex2.75e-092
locus ceruleus2.87e-092
brainstem nucleus2.87e-092
hindbrain nucleus2.87e-092
globus pallidus3.83e-092
pallidum3.83e-092
germ layer1.84e-08560
germ layer / neural crest1.84e-08560
embryonic tissue1.84e-08560
presumptive structure1.84e-08560
germ layer / neural crest derived structure1.84e-08560


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
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
MA0042.11.22641
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.115382
MA0058.11.04727
MA0059.10.404929
MA0060.10.638423
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0282921
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.12.179
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
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
MA0124.12.64084
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
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.20.0828768
MA0150.11.10099
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.0167306
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.21.2885e-05
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

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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