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Coexpression cluster:C1971: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.00991994,MA0004.1;3.75179,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.0418333,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.189508,MA0058.1;3.29768,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;3.16868,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.111822,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;1.2972,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;1.36977,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;2.99362,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;3.50906,MA0113.1;3.1147,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;1.39943,MA0146.1;0.0359558,MA0147.1;1.77656,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.777733,MA0035.2;0.691506,MA0039.2;0.0575907,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.858845,MA0047.2;0.767096,MA0112.2;3.37937,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;1.15604,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.00207114,MA0102.2;1.66336,MA0258.1;1.63655,MA0259.1;1.80881,MA0442.1;0
}}
}}

Revision as of 20:19, 22 January 2013


Full id: C1971_spleen_Endothelial_heart_lung_adipose_mature_locus



Phase1 CAGE Peaks

Hg19::chr6:151004729..151004751,+p7@PLEKHG1
Hg19::chr6:151004757..151004770,+p12@PLEKHG1
Hg19::chr6:151004774..151004794,+p4@PLEKHG1
Hg19::chr6:151004802..151004822,+p3@PLEKHG1
Hg19::chr6:151004835..151004845,+p15@PLEKHG1


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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.95e-69114
neural tube4.31e-3956
neural rod4.31e-3956
future spinal cord4.31e-3956
neural keel4.31e-3956
regional part of nervous system7.28e-3653
regional part of brain7.28e-3653
regional part of forebrain8.42e-3341
forebrain8.42e-3341
anterior neural tube8.42e-3341
future forebrain8.42e-3341
brain grey matter2.53e-3034
gray matter2.53e-3034
telencephalon8.37e-3034
anatomical conduit3.96e-28240
neural plate5.06e-2882
presumptive neural plate5.06e-2882
regional part of telencephalon1.05e-2732
cerebral hemisphere2.26e-2732
tube3.58e-26192
neurectoderm5.25e-2686
brain6.45e-2668
future brain6.45e-2668
central nervous system8.84e-2581
regional part of cerebral cortex1.62e-2222
anatomical cluster1.35e-21373
nervous system6.52e-2189
blood vessel endothelium1.18e-2018
endothelium1.18e-2018
cardiovascular system endothelium1.18e-2018
ecto-epithelium5.41e-20104
neocortex6.56e-2020
pre-chordal neural plate1.19e-1961
cerebral cortex3.86e-1925
pallium3.86e-1925
structure with developmental contribution from neural crest9.71e-19132
simple squamous epithelium6.58e-1622
squamous epithelium2.28e-1325
neural nucleus3.16e-139
nucleus of brain3.16e-139
basal ganglion3.30e-139
nuclear complex of neuraxis3.30e-139
aggregate regional part of brain3.30e-139
collection of basal ganglia3.30e-139
cerebral subcortex3.30e-139
epithelium4.26e-13306
cell layer9.51e-13309
organ system subdivision7.03e-12223
telencephalic nucleus1.49e-107
vessel5.26e-1068
ectoderm-derived structure8.29e-10171
ectoderm8.29e-10171
presumptive ectoderm8.29e-10171
multi-cellular organism8.64e-10656
temporal lobe9.00e-106
endothelial tube1.29e-099
arterial system endothelium1.29e-099
endothelium of artery1.29e-099
anatomical system2.12e-09624
anatomical group2.49e-09625
gyrus6.32e-096
brainstem7.40e-096
lymphoid system1.01e-0810
organ part2.44e-08218
limbic system5.34e-085
posterior neural tube8.88e-0815
chordal neural plate8.88e-0815
vasculature1.00e-0778
vascular system1.00e-0778
multi-tissue structure1.19e-07342
vein1.40e-079
venous blood vessel1.40e-079
venous system1.40e-079
lymphatic vessel3.65e-078
lymph vasculature3.65e-078
lymphatic part of lymphoid system3.65e-078
embryonic structure7.09e-07564
germ layer9.82e-07560
germ layer / neural crest9.82e-07560
embryonic tissue9.82e-07560
presumptive structure9.82e-07560
germ layer / neural crest derived structure9.82e-07560
epiblast (generic)9.82e-07560


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)
MA0003.10.00991994
MA0004.13.75179
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.13.29768
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.13.16868
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.111822
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.12.99362
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.13.50906
MA0113.13.1147
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.11.39943
MA0146.10.0359558
MA0147.11.77656
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.23.37937
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.20.699641
MA0079.20.00207114
MA0102.21.66336
MA0258.11.63655
MA0259.11.80881
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
FOS#235358.99795530889441.69470025615156e-050.000389766130923173
GATA2#2624512.7449317335542.9719152914525e-060.000101366381817116
JUN#3725512.51282919233633.25800591331781e-060.000109268747456968
MAX#414956.452555509007128.93743970843928e-050.00130785661441739



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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