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{{Coexpression_clusters
{
|full_id=C699_medulloblastoma_Lens_neuroblastoma_Ciliary_eye_small_cerebellum
|

Latest revision as of 11:28, 17 September 2013


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)
MA0003.10.514819
MA0004.10.32225
MA0006.12.36084
MA0007.10.305951
MA0009.10.756202
MA0014.10.00958972
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.12.05423
MA0027.12.35633
MA0028.10.583404
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.11.4241
MA0050.10.311321
MA0051.12.78099
MA0052.10.682867
MA0055.12.9155
MA0056.10
MA0057.10.0373953
MA0058.10.240796
MA0059.10.239727
MA0060.12.27824
MA0061.10.605357
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.00012619
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.11.25378
MA0081.11.25193
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.0806254
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.535462
MA0105.10.130274
MA0106.10.452066
MA0107.10.137948
MA0108.21.45646
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.418165
MA0115.10.992167
MA0116.10.140463
MA0117.10.792789
MA0119.10.226505
MA0122.11.9139
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.14.43207
MA0136.10.420617
MA0139.10.0781324
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.783809
MA0145.10.0212759
MA0146.10.0677137
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.20.000717146
MA0138.20.503176
MA0002.20.0954816
MA0137.21.76253
MA0104.20.102626
MA0047.20.440861
MA0112.20.216805
MA0065.20.096411
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.30107
MA0155.10.0793743
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.357736
MA0161.10
MA0162.10.138499
MA0163.10.309131
MA0164.10.478818
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.21.73671e-07
MA0102.21.28978
MA0258.10.117513
MA0259.10.455773
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
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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