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Coexpression cluster:C573: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;7:2.96359950522265:0.00509963245402272:0.0237185710917693!GATA2#2624;10:7.96558233347125:4.53445850821904e-08:2.96725759486146e-06!PBX3#5090;4:5.47862817168603:0.00506854601053335:0.0236002620059783!POLR2A#5430;14:1.87902152948831:0.000866722474671407:0.00646707355377632!SUZ12#23512;12:37.5868356832972:6.61555359962862e-18:1.44847338027592e-15!ZNF263#10127;11:5.65251612544484:2.08255457817443e-07:1.11538419276902e-05
|tf_chipseq_enrich=EP300#2033;7:2.96359950522265:0.00509963245402272:0.0237185710917693!GATA2#2624;10:7.96558233347125:4.53445850821904e-08:2.96725759486146e-06!PBX3#5090;4:5.47862817168603:0.00506854601053335:0.0236002620059783!POLR2A#5430;14:1.87902152948831:0.000866722474671407:0.00646707355377632!SUZ12#23512;12:37.5868356832972:6.61555359962862e-18:1.44847338027592e-15!ZNF263#10127;11:5.65251612544484:2.08255457817443e-07:1.11538419276902e-05
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|tfbs_overrepresentation_for_novel_motifs=0.157827,1.0879,0.907146,0.258928,0.125522,0.25764,0.318839,0.470337,0.463955,5.40049,0.660906,0.355038,0.0400361,0.309388,0.393521,0.431887,0.511522,0.0927064,0.689727,0.306606,1.45484,0.521809,0.251588,0.387475,0.18461,0.374311,0.0323758,0.249905,0.400769,0.0271182,0.217756,2.30854,7.97351,0.0409179,0.104423,38.2137,1.66762,2.84664,0.0891992,2.6888,0.690753,0.205653,0.00613108,0.123709,0.197874,0.173971,0.856196,0.226038,0.18831,0.12756,0.386472,0.329494,0.377869,0.615394,0.758742,0.311792,0.130259,0.2852,0.113556,0.284391,0.582323,0.321692,0.212582,0.48664,2.43004,0.456015,0.843028,1.20113,0.535417,1.04233,0.19602,0.0621482,4.33489,0.756844,0.150647,0.0336796,0.120629,0.471562,0.532468,0.532279,0.0470011,1.21884,0.336303,1.25227,0.70821,0.81194,3.36375,10.4377,2.7746,1.29895,0.932961,0.68283,0.560183,0.0788172,0.12599,1.01826,0.385004,0.599297,0.412954,0.020964,0.0899484,0.555021,0.594155,0.514828,0.445845,0.230832,0.500571,0.306566,0.18443,0.370056,1.49993,0.591605,0.149112,0.241506,0.886618,0.101627,1.5701,0.216858,0.453946,0.275094,0.748992,0.406842,0.255485,0.345739,0.993708,0.472239,0.313614,0.564749,1.85511,0.0864157,0.683478,0.627156,0.803201,0.908,0.945426,1.5144,0.21329,0.250344,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,1.39526,0.432737,1.59165,0.58757,0.0770919,0.169169,2.24574,0.683836,0.774617,2.35519,1.07219,0.394947,0.751217,1.63994,0.164414,0.867287,0.66649,0.531753,0.166635,0.46162,0.891749,1.36088,0.317742,0.0705764
}}
}}

Revision as of 14:19, 26 November 2012


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)

{{{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
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.