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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:26, 17 September 2013


Full id: C573_Lens_small_retina_Ciliary_Retinal_eye_putamen



Phase1 CAGE Peaks

Hg19::chr2:45165994..45166012,-p1@ENST00000444871
Hg19::chr2:45166274..45166281,-p5@ENST00000437916
Hg19::chr2:45166354..45166379,-p1@ENST00000437916
Hg19::chr2:45168617..45168631,-p1@ENST00000456467
Hg19::chr2:45168834..45168847,+p2@SIX3
Hg19::chr2:45168856..45168867,+p7@SIX3
Hg19::chr2:45168875..45168916,+p1@SIX3
Hg19::chr2:45169039..45169058,-p1@ENST00000419364
Hg19::chr2:45169143..45169167,+p5@SIX3
Hg19::chr2:45169172..45169177,+p11@SIX3
Hg19::chr2:45169179..45169190,+p8@SIX3
Hg19::chr2:45169193..45169219,+p3@SIX3
Hg19::chr2:45169233..45169244,+p10@SIX3
Hg19::chr2:45169905..45169915,+p@chr2:45169905..45169915
+
Hg19::chr2:45171888..45171968,+p@chr2:45171888..45171968
+
Hg19::chr8:99076582..99076599,+p6@C8orf47


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:0030178negative regulation of Wnt receptor signaling pathway0.0165135994348287
GO:0030111regulation of Wnt receptor signaling pathway0.0165135994348287
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0165135994348287
GO:0043010camera-type eye development0.0165135994348287
GO:0001654eye development0.0182620981985164
GO:0007423sensory organ development0.027846461792064
GO:0009968negative regulation of signal transduction0.0288641065751627
GO:0007420brain development0.0313002865104596
GO:0016055Wnt receptor signaling pathway0.0313002865104596
GO:0016564transcription repressor activity0.0351194196125316
GO:0007601visual perception0.0351194196125316
GO:0050953sensory perception of light stimulus0.0351194196125316
GO:0007417central nervous system development0.0351194196125316
GO:0003702RNA polymerase II transcription factor activity0.0376898622394913
GO:0016481negative regulation of transcription0.0376898622394913
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0387341045566937
GO:0031324negative regulation of cellular metabolic process0.0435410476447732
GO:0009892negative regulation of metabolic process0.0470583617881392



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
pre-chordal neural plate7.79e-3661
neurectoderm4.27e-2886
neural plate3.02e-2682
presumptive neural plate3.02e-2682
pigment epithelium of eye3.33e-2611
eye1.03e-2121
visual system1.03e-2121
ecto-epithelium3.04e-20104
camera-type eye2.00e-1920
simple eye2.00e-1920
immature eye2.00e-1920
ocular region2.00e-1920
eyeball of camera-type eye2.00e-1920
optic cup2.00e-1920
optic vesicle2.00e-1920
eye primordium2.00e-1920
sense organ1.47e-1824
sensory system1.47e-1824
entire sense organ system1.47e-1824
regional part of forebrain1.82e-1841
forebrain1.82e-1841
anterior neural tube1.82e-1841
future forebrain1.82e-1841
face2.25e-1722
ectoderm-derived structure8.35e-17171
ectoderm8.35e-17171
presumptive ectoderm8.35e-17171
structure with developmental contribution from neural crest1.67e-16132
brain1.35e-1568
future brain1.35e-1568
nervous system3.59e-1589
basal ganglion4.59e-159
nuclear complex of neuraxis4.59e-159
aggregate regional part of brain4.59e-159
collection of basal ganglia4.59e-159
cerebral subcortex4.59e-159
regional part of nervous system8.78e-1553
regional part of brain8.78e-1553
telencephalic nucleus1.00e-147
central nervous system1.02e-1481
neural tube9.84e-1456
neural rod9.84e-1456
future spinal cord9.84e-1456
neural keel9.84e-1456
retina9.29e-136
photoreceptor array9.29e-136
posterior segment of eyeball9.29e-136
atypical epithelium1.14e-124
corpus striatum2.19e-124
striatum2.19e-124
ventral part of telencephalon2.19e-124
future corpus striatum2.19e-124
telencephalon7.55e-1234
ectodermal placode1.91e-1131
neural nucleus2.87e-119
nucleus of brain2.87e-119
regional part of telencephalon5.69e-1132
cerebral hemisphere5.69e-1132
brain grey matter3.58e-1034
gray matter3.58e-1034
ciliary epithelium5.29e-103
ciliary body5.29e-103
pigmented layer of retina5.45e-103
presumptive retinal pigmented epithelium5.45e-103
caudate-putamen7.93e-103
dorsal striatum7.93e-103
anterior segment of eyeball9.22e-1014
diencephalon9.22e-107
future diencephalon9.22e-107
vasculature of organ8.07e-0911
vasculature of eye2.06e-086
uvea2.06e-086
vasculature of head2.06e-086
layer of retina1.46e-074
cuboidal epithelium1.88e-074
transparent eye structure1.88e-074
simple cuboidal epithelium1.88e-074
cranial placode1.88e-074
lens of camera-type eye1.88e-074
epithelium of lens1.88e-074
lens placode1.88e-074
lens vesicle1.88e-074
caudate nucleus4.45e-072
future caudate nucleus4.45e-072
pituitary gland8.60e-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)
MA0003.10.038097
MA0004.10.238283
MA0006.10.392773
MA0007.10.223897
MA0009.10.644692
MA0014.11.05669
MA0017.10.150184
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.11.54944
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.0786451
MA0050.11.88167
MA0051.14.19733
MA0052.10.574006
MA0055.10.499384
MA0056.10
MA0057.110.1205
MA0058.10.167587
MA0059.10.499176
MA0060.10.464905
MA0061.10.0461955
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.11.71484
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.113.2591
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.12.19686
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.0965118
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.10.211423
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.403202
MA0103.10.118522
MA0105.10.0129929
MA0106.10.355999
MA0107.10.285979
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.10.278245
MA0115.10.874839
MA0116.10.0861811
MA0117.10.680135
MA0119.10.155538
MA0122.11.67968
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.10.652922
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.0738381
MA0145.10.113672
MA0146.10.0055415
MA0147.11.03443
MA0148.10.257816
MA0149.13.89598
MA0062.20.168482
MA0035.20.286421
MA0039.20.562413
MA0138.20.403517
MA0002.20.196222
MA0137.20.138998
MA0104.20.803527
MA0047.20.345656
MA0112.20.390337
MA0065.20.667633
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.0124644
MA0155.10.0948197
MA0156.10.140505
MA0157.10.442323
MA0158.10
MA0159.10.29763
MA0160.10.26995
MA0161.10
MA0162.11.75154
MA0163.10.207536
MA0164.10.380804
MA0080.20.126365
MA0018.20.357181
MA0099.20.292649
MA0079.221.6977
MA0102.21.16862
MA0258.10.0689091
MA0259.10.0929051
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
EP300#203372.963599505222650.005099632454022720.0237185710917693
GATA2#2624107.965582333471254.53445850821904e-082.96725759486146e-06
PBX3#509045.478628171686030.005068546010533350.0236002620059783
POLR2A#5430141.879021529488310.0008667224746714070.00646707355377632
SUZ12#235121237.58683568329726.61555359962862e-181.44847338027592e-15
ZNF263#10127115.652516125444842.08255457817443e-071.11538419276902e-05



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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