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Coexpression cluster:C699: Difference between revisions

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|tf_chipseq_enrich=REST#5978;7:5.62918341774135:6.32358000930756e-05:0.00103224190777129!SUZ12#23512;12:50.1157809110629:3.91454139263279e-21:1.04293568496218e-18
|tf_chipseq_enrich=REST#5978;7:5.62918341774135:6.32358000930756e-05:0.00103224190777129!SUZ12#23512;12:50.1157809110629:3.91454139263279e-21:1.04293568496218e-18
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|tfbs_overrepresentation_for_novel_motifs=0.649083,0.00275938,0.223258,3.40273,0.190185,0.344001,0.411652,0.104517,0.687431,0.302415,0.317729,0.451026,1.41978,0.401301,0.189126,0.207465,1.49799,0.148925,0.0839658,0.848367,1.18892,0.594884,0.337221,0.18624,0.260754,0.471832,0.858875,0.335332,0.192587,0.454328,0.298956,0.65246,0.396376,0.0778977,0.163884,0.117596,0.161511,0.912597,0.871544,0.0916487,0.162847,0.285097,0.658594,0.187953,0.00327556,0.24831,1.06122,1.50384,0.188988,0.192687,1.21719,0.423285,0.978083,0.725869,0.873575,1.04226,0.195993,0.374657,0.0564659,0.373762,0.691524,0.414771,0.103208,0.591384,1.9302,0.559038,0.959746,1.32257,1.5504,2.61518,0.273995,0.108268,0.0373297,0.871629,0.257259,1.31915,0.472331,0.575479,0.639503,1.31112,0.0868483,0.590372,1.10045,0.345708,0.821696,0.180819,5.18619,0.0540708,0.508983,1.42111,1.05129,0.795567,2.70755,0.812938,0.190761,0.432898,0.0830795,0.709167,0.51326,0.0463096,0.145361,0.663075,5.44298,0.621018,0.54826,0.313822,0.606045,0.398205,0.260543,0.177931,0.232335,0.701175,1.17167,0.325885,1.00416,0.938502,0.104888,4.04451,0.556847,0.132787,0.863578,0.506732,0.341589,0.44095,1.11293,2.41067,0.405934,0.673222,0.905059,0.140769,0.796235,0.301402,0.919079,0.437919,1.06395,0.0507172,1.45145,0.335825,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,0.282284,0.403378,0.133101,0.0163338,0.796604,0.663597,0.414334,1.19239,0.494,0.530398,2.86165,0.237047,0.984474,0.778717,1.54238,8.67481,0.564971,0.429983,0.120139,0.410452,0.51183
}}
}}

Revision as of 14:24, 26 November 2012


Full id: C699_medulloblastoma_Lens_neuroblastoma_Ciliary_eye_small_cerebellum



Phase1 CAGE Peaks

Hg19::chr13:36045322..36045356,+p9@NBEA
Hg19::chr13:36046061..36046077,+p@chr13:36046061..36046077
+
Hg19::chr13:36046127..36046134,+p@chr13:36046127..36046134
+
Hg19::chr13:36046521..36046554,+p@chr13:36046521..36046554
+
Hg19::chr13:36050790..36050807,-p2@MAB21L1
Hg19::chr13:36050819..36050834,-p1@MAB21L1
Hg19::chr13:36050881..36050887,+p3@NBEA
Hg19::chr13:36050940..36050952,+p2@NBEA
Hg19::chr13:36050956..36050969,+p4@NBEA
Hg19::chr13:36050976..36050990,+p8@NBEA
Hg19::chr13:36052762..36052767,-p@chr13:36052762..36052767
-
Hg19::chr13:36052779..36052793,-p@chr13:36052779..36052793
-


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:0005802trans-Golgi network0.0296627598117251



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
posterior neural tube9.35e-2715
chordal neural plate9.35e-2715
pigment epithelium of eye2.13e-2211
segmental subdivision of hindbrain2.29e-1912
hindbrain2.29e-1912
presumptive hindbrain2.29e-1912
neural plate1.81e-1882
presumptive neural plate1.81e-1882
segmental subdivision of nervous system9.75e-1813
neurectoderm2.66e-1786
eye1.50e-1621
visual system1.50e-1621
regional part of metencephalon2.47e-169
metencephalon2.47e-169
future metencephalon2.47e-169
face1.37e-1522
camera-type eye2.62e-1420
simple eye2.62e-1420
immature eye2.62e-1420
ocular region2.62e-1420
eyeball of camera-type eye2.62e-1420
optic cup2.62e-1420
optic vesicle2.62e-1420
eye primordium2.62e-1420
subdivision of head3.35e-1449
sense organ3.70e-1424
sensory system3.70e-1424
entire sense organ system3.70e-1424
ectoderm-derived structure7.67e-14171
ectoderm7.67e-14171
presumptive ectoderm7.67e-14171
atypical epithelium9.93e-144
anterior region of body3.08e-1362
craniocervical region3.08e-1362
ecto-epithelium3.56e-13104
structure with developmental contribution from neural crest5.97e-13132
brainstem1.75e-126
head6.84e-1256
ciliary epithelium8.83e-113
ciliary body8.83e-113
pons6.29e-103
pigmented layer of retina6.69e-103
presumptive retinal pigmented epithelium6.69e-103
spinal cord2.03e-093
dorsal region element2.03e-093
dorsum2.03e-093
vasculature of eye3.91e-096
uvea3.91e-096
vasculature of head3.91e-096
cerebellum9.73e-096
rhombic lip9.73e-096
organ segment1.02e-0898
retina1.19e-086
photoreceptor array1.19e-086
posterior segment of eyeball1.19e-086
ectodermal placode1.84e-0831
neural tube2.30e-0856
neural rod2.30e-0856
future spinal cord2.30e-0856
neural keel2.30e-0856
anterior segment of eyeball6.05e-0814
layer of retina1.62e-074
nervous system2.24e-0789
locus ceruleus3.82e-072
brainstem nucleus3.82e-072
hindbrain nucleus3.82e-072
breast4.16e-0710
throat6.80e-072


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)

{{{tfbs_overrepresentation_jaspar}}}



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
REST#597875.629183417741356.32358000930756e-050.00103224190777129
SUZ12#235121250.11578091106293.91454139263279e-211.04293568496218e-18



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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