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Coexpression cluster:C1143: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,1.1011,0.384703,0.529489,1.62733,0.52784,0.604235,0.226729,0.224331,0.773341,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.786991,1.08139,0.66776,0.384762,0.23059,0.520063,0.338096,0.430372,0.670692,2.1826,0.517892,1.63811,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.232776,0.825031,0.529001,0.282922,0.207499,0.307642,0.459366,0.254304,0.340293,0.109128,0.415364,0.60533,0.486696,0.237549,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.924875,0.562713,0.459282,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.369103,1.0929,0.179863,0.168304,0.473656,0.782748,0.850825,0.424224,0.580264,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,2.17049,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,1.92716,0.327379,1.81048,0.915771,0.379203,0.507004,1.22894,1.48924,0.155979,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,3.79029,0.47854,1.14174,2.59532,1.28996,0.854586,0.469685,1.28879,4.50163,2.10682,1.70417,1.21002,0.59959,0.920609,1.78463,0.554217,0.738579,1.94751,2.99223,0.722945,0.345641,0.0685123,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,1.81801,0.624608,0.24928,0.602897,0.00626991
|tfbs_overrepresentation_jaspar=MA0003.1;0.110456,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;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.382278,MA0050.1;1.22833,MA0051.1;1.46692,MA0052.1;0.896548,MA0055.1;1.4376,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;1.86058,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;0.000265001,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;0.538456,MA0089.1;0,MA0090.1;0.436918,MA0091.1;1.26109,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.918548,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;1.17486,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;0.547495,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;1.30855,MA0145.1;0.0807715,MA0146.1;0.162729,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;1.38583,MA0039.2;0.00276064,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;1.70023,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;2.39586,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.071478,MA0156.1;0.959643,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.0249953,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;9.15802e-07,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:44, 22 January 2013


Full id: C1143_parotid_salivary_corpus_optic_temporal_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr11:49230087..49230098,-p7@FOLH1B
p7@FOLH1
Hg19::chr11:49230144..49230164,-p1@FOLH1B
p1@FOLH1
Hg19::chr11:49230172..49230183,-p6@FOLH1B
p6@FOLH1
Hg19::chr11:49230184..49230198,-p5@FOLH1B
p5@FOLH1
Hg19::chr13:88323717..88323728,+p@chr13:88323717..88323728
+
Hg19::chr15:101402041..101402067,+p1@ENST00000558475
p1@ENST00000558641
p1@ENST00000559673
Hg19::chr3:138022481..138022501,-p@chr3:138022481..138022501
-


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
adult organism3.63e-67114
neural tube2.06e-6056
neural rod2.06e-6056
future spinal cord2.06e-6056
neural keel2.06e-6056
regional part of nervous system1.39e-5453
regional part of brain1.39e-5453
central nervous system4.47e-4881
brain1.77e-4668
future brain1.77e-4668
nervous system2.68e-4489
regional part of forebrain3.25e-4441
forebrain3.25e-4441
anterior neural tube3.25e-4441
future forebrain3.25e-4441
brain grey matter1.28e-4334
gray matter1.28e-4334
telencephalon1.47e-4334
neural plate1.07e-4182
presumptive neural plate1.07e-4182
regional part of telencephalon1.80e-3932
cerebral hemisphere2.43e-3932
neurectoderm3.69e-3986
ecto-epithelium3.88e-35104
pre-chordal neural plate5.31e-3161
organ system subdivision5.86e-31223
regional part of cerebral cortex2.04e-3022
structure with developmental contribution from neural crest1.05e-28132
ectoderm-derived structure3.18e-28171
ectoderm3.18e-28171
presumptive ectoderm3.18e-28171
neocortex1.39e-2620
cerebral cortex3.00e-2625
pallium3.00e-2625
anatomical cluster1.12e-20373
neural nucleus5.66e-209
nucleus of brain5.66e-209
anatomical conduit2.97e-18240
tube4.93e-18192
posterior neural tube1.12e-1615
chordal neural plate1.12e-1615
telencephalic nucleus1.16e-157
basal ganglion2.58e-159
nuclear complex of neuraxis2.58e-159
aggregate regional part of brain2.58e-159
collection of basal ganglia2.58e-159
cerebral subcortex2.58e-159
brainstem1.55e-146
multi-tissue structure1.59e-14342
segmental subdivision of nervous system3.18e-1313
organ1.98e-12503
epithelium2.16e-11306
segmental subdivision of hindbrain2.70e-1112
hindbrain2.70e-1112
presumptive hindbrain2.70e-1112
cell layer3.91e-11309
occipital lobe4.25e-115
organ part3.60e-10218
gyrus2.20e-096
corpus striatum3.17e-094
striatum3.17e-094
ventral part of telencephalon3.17e-094
future corpus striatum3.17e-094
anatomical system4.15e-09624
developing anatomical structure4.36e-09581
embryo4.38e-09592
germ layer4.63e-09560
germ layer / neural crest4.63e-09560
embryonic tissue4.63e-09560
presumptive structure4.63e-09560
germ layer / neural crest derived structure4.63e-09560
epiblast (generic)4.63e-09560
anatomical group4.65e-09625
embryonic structure7.49e-09564
pons3.50e-083
multi-cellular organism3.57e-08656
medulla oblongata4.94e-083
myelencephalon4.94e-083
future myelencephalon4.94e-083
spinal cord1.14e-073
dorsal region element1.14e-073
dorsum1.14e-073
temporal lobe1.19e-076
parietal lobe1.39e-075
limbic system1.74e-075
caudate-putamen2.93e-073
dorsal striatum2.93e-073


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)
MA0003.10.110456
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
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.11.22833
MA0051.11.46692
MA0052.10.896548
MA0055.11.4376
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.11.86058
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
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.11.26109
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
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
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.11.30855
MA0145.10.0807715
MA0146.10.162729
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.21.38583
MA0039.20.00276064
MA0138.20.704862
MA0002.20.213296
MA0137.21.70023
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.12.39586
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.29.15802e-07
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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