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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:21, 17 September 2013


Full id: C369_Lens_eye_Ciliary_retina_H9_Retinal_Renal



Phase1 CAGE Peaks

Hg19::chr11:31671561..31671580,+p@chr11:31671561..31671580
+
Hg19::chr13:104778247..104778293,+p@chr13:104778247..104778293
+
Hg19::chr13:36052713..36052724,-p@chr13:36052713..36052724
-
Hg19::chr15:79501729..79501736,+p1@MIR184
Hg19::chr15:95888661..95888665,+p@chr15:95888661..95888665
+
Hg19::chr19:40920692..40920700,-p@chr19:40920692..40920700
-
Hg19::chr19:51891222..51891233,-p1@LIM2
Hg19::chr1:147374915..147374932,+p1@GJA8
Hg19::chr20:35861148..35861151,+p@chr20:35861148..35861151
+
Hg19::chr22:25595823..25595826,+p1@CRYBB3
Hg19::chr22:25615541..25615544,+p2@CRYBB2
Hg19::chr2:45162900..45162914,-p1@ENST00000432125
Hg19::chr2:45162929..45162943,-p2@ENST00000432125
Hg19::chr2:45166428..45166437,-p4@ENST00000437916
Hg19::chr2:63196015..63196016,+p@chr2:63196015..63196016
+
Hg19::chr2:66670833..66670853,+p@chr2:66670833..66670853
+
Hg19::chr3:150690508..150690520,-p1@CLRN1
Hg19::chr3:150690540..150690556,-p2@CLRN1
Hg19::chr3:150690809..150690822,-p3@CLRN1
Hg19::chr3:62358596..62358618,-p3@FEZF2
Hg19::chr3:62358748..62358751,-p7@FEZF2
Hg19::chr3:98705008..98705016,-p@chr3:98705008..98705016
-
Hg19::chr3:98705040..98705081,-p@chr3:98705040..98705081
-
Hg19::chr4:8873531..8873542,-p4@HMX1
Hg19::chr4:8873545..8873583,-p1@HMX1
Hg19::chr6:80543084..80543091,-p@chr6:80543084..80543091
-
Hg19::chr8:123875589..123875604,+p24@ZHX2
Hg19::chr8:123875629..123875640,+p21@ZHX2
Hg19::chr8:36807609..36807626,-p@chr8:36807609..36807626
-
Hg19::chr9:75848662..75848671,-p@chr9:75848662..75848671
-


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:0005212structural constituent of eye lens1.27415068449798e-06
GO:0007601visual perception4.62678414592927e-06
GO:0050953sensory perception of light stimulus4.62678414592927e-06
GO:0007600sensory perception0.0010352899857421
GO:0032501multicellular organismal process0.0010352899857421
GO:0050877neurological system process0.0022444358804151
GO:0003008system process0.00405747896702666
GO:0050957equilibrioception0.0263556467090979
GO:0007043intercellular junction assembly0.0364949867660109
GO:0045494photoreceptor cell maintenance0.0364949867660109
GO:0050885neuromuscular process controlling balance0.0364949867660109
GO:0045216intercellular junction assembly and maintenance0.0364949867660109
GO:0030054cell junction0.0364949867660109
GO:0050905neuromuscular process0.0420995890852978
GO:0007028cytoplasm organization and biogenesis0.0420995890852978
GO:0005922connexon complex0.0448624819908534
GO:0006402mRNA catabolic process0.0448624819908534
GO:0005921gap junction0.0470365975887916
GO:0043010camera-type eye development0.0470365975887916



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
atypical epithelium5.61e-884
pigment epithelium of eye1.20e-7111
ciliary epithelium9.82e-673
ciliary body9.82e-673
eye2.15e-6621
visual system2.15e-6621
vasculature of eye6.44e-596
uvea6.44e-596
vasculature of head6.44e-596
sense organ4.06e-5824
sensory system4.06e-5824
entire sense organ system4.06e-5824
anterior segment of eyeball2.24e-5614
camera-type eye1.74e-5320
simple eye1.74e-5320
immature eye1.74e-5320
ocular region1.74e-5320
eyeball of camera-type eye1.74e-5320
optic cup1.74e-5320
optic vesicle1.74e-5320
eye primordium1.74e-5320
face1.22e-4822
ectodermal placode1.45e-3431
vasculature of organ1.90e-3211
iris epithelium4.10e-231
iris4.10e-231
cuboidal epithelium5.75e-234
transparent eye structure5.75e-234
simple cuboidal epithelium5.75e-234
cranial placode5.75e-234
lens of camera-type eye5.75e-234
epithelium of lens5.75e-234
lens placode5.75e-234
lens vesicle5.75e-234
subdivision of head6.84e-2249
head3.73e-1956
anterior region of body2.68e-1762
craniocervical region2.68e-1762
pre-chordal neural plate2.68e-1761
neural plate6.68e-1382
presumptive neural plate6.68e-1382
neurectoderm2.65e-1286
external ectoderm5.22e-128
organ segment6.62e-1198
ecto-epithelium3.62e-10104
structure with developmental contribution from neural crest5.53e-08132


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)
MA0003.10.29554
MA0004.10.0961566
MA0006.10.908257
MA0007.10.0871398
MA0009.10.417521
MA0014.10.0116099
MA0017.11.07347
MA0019.10.180682
MA0024.10.332558
MA0025.10.531977
MA0027.11.95983
MA0028.10.149896
MA0029.10.347825
MA0030.10.338746
MA0031.10.288912
MA0038.10.464214
MA0040.10.352485
MA0041.10.105506
MA0042.10.0896515
MA0043.10.417784
MA0046.10.408463
MA0048.10.57305
MA0050.10.0900741
MA0051.10.150026
MA0052.10.355576
MA0055.10.615824
MA0056.10
MA0057.10.749073
MA0058.10.0546193
MA0059.10.0541371
MA0060.10.0459286
MA0061.10.579374
MA0063.10
MA0066.10.152817
MA0067.10.697961
MA0068.10.0580596
MA0069.10.405267
MA0070.10.396023
MA0071.10.407159
MA0072.10.392323
MA0073.10.0618507
MA0074.10.89351
MA0076.10.060743
MA0077.11.00303
MA0078.10.612611
MA0081.10.19978
MA0083.10.423797
MA0084.10.873335
MA0087.10.390315
MA0088.10.941584
MA0089.10
MA0090.10.508642
MA0091.10.661948
MA0092.10.574995
MA0093.10.0341631
MA0095.10
MA0098.10
MA0100.10.161006
MA0101.10.140397
MA0103.10.0306888
MA0105.10.309448
MA0106.10.178189
MA0107.10.0779652
MA0108.20.781414
MA0109.10
MA0111.10.538416
MA0113.10.188804
MA0114.11.28653
MA0115.11.52011
MA0116.10.969948
MA0117.10.449155
MA0119.10.407887
MA0122.10.471243
MA0124.10.590699
MA0125.10.516292
MA0130.10
MA0131.10.226279
MA0132.10
MA0133.10
MA0135.10.443024
MA0136.10.156833
MA0139.10.18088
MA0140.10.128473
MA0141.10.437416
MA0142.10.265252
MA0143.11.66405
MA0144.10.567573
MA0145.11.94091
MA0146.10.344955
MA0147.10.0831159
MA0148.10.1088
MA0149.10.389467
MA0062.20.0300684
MA0035.20.128078
MA0039.20.089146
MA0138.20.214585
MA0002.20.113455
MA0137.20.643617
MA0104.20.0455118
MA0047.20.170483
MA0112.20.413602
MA0065.21.98829
MA0150.10.495826
MA0151.10
MA0152.10.412817
MA0153.10.501603
MA0154.10.450486
MA0155.10.157152
MA0156.10.15867
MA0157.10.245386
MA0158.10
MA0159.10.211902
MA0160.10.373329
MA0161.10
MA0162.10.161648
MA0163.10.267894
MA0164.10.196993
MA0080.20.137324
MA0018.20.179075
MA0099.20.413335
MA0079.21.29071
MA0102.20.908736
MA0258.10.0584056
MA0259.10.0895432
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
CTBP2#148836.271700033932810.01192664700016820.0433903607500111
SUZ12#2351246.682104121475050.002866208855127340.0155317795164554



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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