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Coexpression cluster:C573: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!1.02e-12!143;DOID:305!1.41e-09!106
|ontology_enrichment_disease=DOID:0050687!1.02e-12!143;DOID:305!1.41e-09!106
|ontology_enrichment_uberon=UBERON:0002346!6.65e-29!90;UBERON:0000073!1.12e-28!94;UBERON:0001016!1.12e-28!94;UBERON:0003075!1.22e-27!86;UBERON:0007284!1.22e-27!86;UBERON:0005743!5.96e-26!86;UBERON:0003056!6.58e-25!61;UBERON:0001017!9.45e-23!82;UBERON:0002616!9.36e-21!59;UBERON:0001049!3.54e-20!57;UBERON:0005068!3.54e-20!57;UBERON:0006241!3.54e-20!57;UBERON:0007135!3.54e-20!57;UBERON:0000955!1.35e-19!69;UBERON:0006238!1.35e-19!69;UBERON:0002780!2.91e-19!41;UBERON:0001890!2.91e-19!41;UBERON:0006240!2.91e-19!41;UBERON:0000924!1.32e-18!173;UBERON:0006601!1.32e-18!173;UBERON:0003080!1.81e-18!42;UBERON:0004121!1.65e-17!169;UBERON:0002020!2.57e-14!34;UBERON:0003528!2.57e-14!34;UBERON:0001893!3.49e-14!34;UBERON:0002791!5.44e-14!33;UBERON:0000033!7.16e-14!123;UBERON:0000153!3.48e-13!129;UBERON:0007811!3.48e-13!129;UBERON:0001869!5.28e-13!32;UBERON:0007625!8.25e-12!11;UBERON:0007023!4.63e-11!115;UBERON:0002104!5.78e-09!21;UBERON:0002420!1.02e-08!9;UBERON:0007245!1.02e-08!9;UBERON:0010009!1.02e-08!9;UBERON:0010011!1.02e-08!9;UBERON:0000454!1.02e-08!9;UBERON:0000970!2.16e-08!20;UBERON:0000956!2.40e-08!25;UBERON:0000203!2.40e-08!25;UBERON:0002308!2.71e-08!9;UBERON:0000125!2.71e-08!9;UBERON:0001032!5.45e-08!24;UBERON:0004456!5.45e-08!24;UBERON:0000019!1.36e-07!19;UBERON:0000047!1.36e-07!19;UBERON:0004088!1.36e-07!19;UBERON:0003072!1.36e-07!19;UBERON:0003071!1.36e-07!19;UBERON:0004128!1.36e-07!19;UBERON:0000020!1.89e-07!23;UBERON:0009663!2.18e-07!7;UBERON:0001894!5.44e-07!7;UBERON:0006222!5.44e-07!7
|ontology_enrichment_uberon=UBERON:0002346!6.65e-29!90;UBERON:0000073!1.12e-28!94;UBERON:0001016!1.12e-28!94;UBERON:0003075!1.22e-27!86;UBERON:0007284!1.22e-27!86;UBERON:0005743!5.96e-26!86;UBERON:0003056!6.58e-25!61;UBERON:0001017!9.45e-23!82;UBERON:0002616!9.36e-21!59;UBERON:0001049!3.54e-20!57;UBERON:0005068!3.54e-20!57;UBERON:0006241!3.54e-20!57;UBERON:0007135!3.54e-20!57;UBERON:0000955!1.35e-19!69;UBERON:0006238!1.35e-19!69;UBERON:0002780!2.91e-19!41;UBERON:0001890!2.91e-19!41;UBERON:0006240!2.91e-19!41;UBERON:0000924!1.32e-18!173;UBERON:0006601!1.32e-18!173;UBERON:0003080!1.81e-18!42;UBERON:0004121!1.65e-17!169;UBERON:0002020!2.57e-14!34;UBERON:0003528!2.57e-14!34;UBERON:0001893!3.49e-14!34;UBERON:0002791!5.44e-14!33;UBERON:0000033!7.16e-14!123;UBERON:0000153!3.48e-13!129;UBERON:0007811!3.48e-13!129;UBERON:0001869!5.28e-13!32;UBERON:0007625!8.25e-12!11;UBERON:0007023!4.63e-11!115;UBERON:0002104!5.78e-09!21;UBERON:0002420!1.02e-08!9;UBERON:0007245!1.02e-08!9;UBERON:0010009!1.02e-08!9;UBERON:0010011!1.02e-08!9;UBERON:0000454!1.02e-08!9;UBERON:0000970!2.16e-08!20;UBERON:0000956!2.40e-08!25;UBERON:0000203!2.40e-08!25;UBERON:0002308!2.71e-08!9;UBERON:0000125!2.71e-08!9;UBERON:0001032!5.45e-08!24;UBERON:0004456!5.45e-08!24;UBERON:0000019!1.36e-07!19;UBERON:0000047!1.36e-07!19;UBERON:0004088!1.36e-07!19;UBERON:0003072!1.36e-07!19;UBERON:0003071!1.36e-07!19;UBERON:0004128!1.36e-07!19;UBERON:0000020!1.89e-07!23;UBERON:0009663!2.18e-07!7;UBERON:0001894!5.44e-07!7;UBERON:0006222!5.44e-07!7
|tfbs_overrepresentation=0.0111122,0.042055,8.16376e-72,0.229529,0.000237098,0.540191,0.208995,7.63183e-14,0.0139964,0.129676,0.551034,0.394962,0.102778,0.0363843,0.0561964,2.88706e-05,4.9338e-12,0.423786,0.251434,0.125167,2.98016e-07,0.00757994,0.000112798,0.016912,0.00163483,0.725936,0.714378,0.397832,0.0514841,0.407128,0.00165067,0.0278827,0.0924848,8.01402e-07,0.307297,0.0122629,0.0019537,0.208823,0.495358,0.308005,0.000246993,0.124451,7.32783e-11,0.661967,0.00540143,0.178709,0.186745,0.289326,3.48977e-07,8.26705e-05,0.224728,0.257015,0.000693694,1.30573e-06,0.03223,0.188544,0.123976,0.364476,0.0099354,0.448463,0.147274,0.056921,0.458354,0.343783,0.258646,0.241421,0.0308569,0.281114,0.0842067,0.622754,6.1497e-20,0.311847,0.0893995,0.00515227,0.0392318,0.0879723,0.417941,0.212019,0.18328,0.0380772,0.414964,0.0506833,0.206756,0.478285,1.36795e-14,0.00110547,0.000497384,0.00184288,2.29493e-18,3.0846e-05,0.380089,0.237575,0.414114,0.000152188,4.28847e-08,0.139211,2.48748e-52,0.58918,0.404948,0.0944974,0.270762,0.00042496,0.557812,0.182452,0.732569,0.199788,0.309129,0.000470609,0.000225026,0.000349958,0.0946672,0.0150603,0.0019678,0.0907785,0.434001,0.000892681,0.00558386,1.6494e-09,0.0471816,0.373123,8.41025e-06,4.45841e-15,2.16042e-05,0.380183,0.437844,5.09063e-13,0.397713,0.0764104,0.0812583,0.00808459,0.00459283,2.92123e-07,0.26965,0.115676,0.511785,0.000425422,0.300698,0.261847,1.32638e-06,0.0209147,0.115627,0.165621,0.000272171,0.229177,2.16643e-09,0.00705197,0.018899,0.374539,0.190907,6.68603e-07,0.697118,0.201031,0.0230994,0.000444098,0.00176746,0.00486527,0.339268,0.402204,0.246562,0.0148307,0.00296657,0.0171009,0.00472755,0.000258891,4.87746e-11,5.88272e-05,7.89515e-05,0.00654275,0.197229,3.75081e-09,0.00459944,0.187726,2.95894e-14,0.0362346,9.98438e-05,0.0146509,0.00932979,0.000126013,0.000111104,0.175944,0.0666209,0.501819,0.137747,6.27826e-05,6.75166e-05,0.031147,0.659776,0.00148086,0.0787222,0.0833974,0.0235555,0.000153874,0.0340924,0.0521283,0.47141,0.226754,0.071057,0.282243,2.74403e-06,0.00375973,0.00173777,0.044369,0.000685519,0.283537,0.000163751,7.20556e-06,0.508206,0.21962,0.708367,0.0892892,0.221518,0.00312294,0.0327903,0.472137,6.42037e-13,0.259717,0.615816,0.433065,0.00538131,3.21459e-05,0.000205308,4.1352e-14,0.0137036,0.607965,0.335836,0.0368724,0.190228,7.60582e-07,0.282924,0.280653,0.0170413,5.06882e-11,0.0223506,0.00930305,0.000240203,0.406517,0.227421,1.84889e-14,0.24665,0.000385127,0.658533,1.48655e-07,0.424459,0.0790987,6.50474e-05,0.045264,0.364577,0.00401808,4.55789e-15,0.143322,0.603019,0.664489,0.0254392,2.4113e-05,0.105923,0.0675142,0.453931,3.75188e-05,0.319314,8.64665e-47,0.288882,0.0852649,0.000458952,0.518607,4.41844e-05,0.362943,0.0758566,0.000197271,0.00494681,0.0666558,1.98811e-25,0.0483541,2.14423e-25,0.0156684,0.383097,0.00126452,0.171164,1.38058e-29,2.89928e-52,1.4966e-21,5.16403e-40,5.3608e-14,4.94846e-50,1.61634e-19,3.1235e-14,0.00326734,0.801526,0.00158288,0.0140608,0.0502572,3.16589e-10,0.882519,0.135264,0.00163345,0.0238617,7.06706e-06,0.0921129,0.000652981,0.000618607,7.12053e-10,2.97254e-05,0.0111622,0.000993931,0.0963099,0.289816,0.0306656,0.462829,0.882698,0.00234852,0.570106,0.0148417,0.644162,2.06348e-28,0.568053,0.000227959,0.236204,0.00924746,1.49675e-14,0.0733658,0.0314673,0.000173722,0.143163,0.00121292,0.154347,0.036718,2.04186e-54,0.0349572,0.59826,4.90993e-25,3.82668e-06,0.000118615,2.46745e-38,0.0719378,1.11505e-08,4.80971e-34,0.00136243,0.0141049,0.0194387,1.91157e-36,0.658307,1.70723e-37,5.77372e-21,0.0373544,0.512229,0.00365373,0.665578,0.0282556,4.6234e-32,0.00769365,0.274376,0.318483,5.57671e-30,0.205209,0.782292,1.69272e-26,0.25769,0.613461,0.309372,1.24912e-08,0.0975135,4.51789e-35,1.8247e-61,0.0208364,5.98444e-08,0.706172,0.250355,1.05059e-12,0.613692,0.731719,0.000238094,1.33688e-14,0.00206951,0.00871919,0.0137481,4.64628e-35,0.339643,1.35395e-17,0.0030899,0.655766,1.59256e-07,0.00273453,1.1231e-18,3.27988e-59,4.95892e-15,1.03851e-53,6.31935e-07,0.401513,0.642097,0.00134624,0.0137827,1.88019e-30,0.0759435,0.000300176,0.0292182,0.346824,6.39233e-08,1.79737e-05,0.565819,0.567792,0.00037255,0.246033,0.00161894,9.34741e-06,0.458832,0.0601865,0.224579,0.00856884,0.798182,0.537988,0.425093,0.791622,0.0404761,0.832396,0.389684,0.0484648,3.63547e-15,0.0621319,6.9236e-15,0.360749,0.000534787,2.31912e-12,0.907047,0.0501913,4.45046e-08,0.00948272,4.48091e-05,0.00236299,6.79314e-42,0.708216,9.62998e-35,5.05772e-39,0.0906691,6.35e-05,0.0254004,2.74465e-22,0.259384,0.00967898,0.40657,3.81369e-06,0.60444,0.42658,0.00109003,0.411464,0.00106355,0.00172575,0.279289,3.0244e-10,1.72975e-31,2.67832e-05,0.39741,0.668344,0.262766,0.0621147,0.102336,0.0899469,0.868267,0.320036,3.77965e-08,0.680381,0.35151,0.2711,0.0520218,0.00266733,1.04305e-16,1.20331e-21,0.014433,0.00619182,0.0265112,1.36288e-12,0.211334,5.91664e-06,0.513824,0.000153013,0.452784,0.00189238,0.292395,6.4702e-13,0.0918879,2.46066e-09,0.0022047,0.0520105,0.224195,0.628872,0.477458,0.445122,0.3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}}
}}

Revision as of 20:32, 8 August 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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neurectoderm6.65e-2990
regional part of nervous system1.12e-2894
nervous system1.12e-2894
neural plate1.22e-2786
presumptive neural plate1.22e-2786
pre-chordal neural plate6.58e-2561
central nervous system9.45e-2382
regional part of brain9.36e-2159
neural tube3.54e-2057
neural rod3.54e-2057
future spinal cord3.54e-2057
neural keel3.54e-2057
brain1.35e-1969
future brain1.35e-1969
regional part of forebrain2.91e-1941
forebrain2.91e-1941
future forebrain2.91e-1941
ectoderm1.32e-18173
presumptive ectoderm1.32e-18173
anterior neural tube1.81e-1842
ectoderm-derived structure1.65e-17169
gray matter2.57e-1434
brain grey matter2.57e-1434
telencephalon3.49e-1434
regional part of telencephalon5.44e-1433
head7.16e-14123
anterior region of body3.48e-13129
craniocervical region3.48e-13129
cerebral hemisphere5.28e-1332
pigment epithelium of eye8.25e-1211
adult organism4.63e-11115
visual system5.78e-0921
basal ganglion1.02e-089
nuclear complex of neuraxis1.02e-089
aggregate regional part of brain1.02e-089
collection of basal ganglia1.02e-089
cerebral subcortex1.02e-089
eye2.16e-0820
cerebral cortex2.40e-0825
pallium2.40e-0825
nucleus of brain2.71e-089
neural nucleus2.71e-089
sensory system5.45e-0824
entire sense organ system5.45e-0824
camera-type eye1.36e-0719
simple eye1.36e-0719
ocular region1.36e-0719
optic cup1.36e-0719
eye primordium1.36e-0719
optic vesicle1.36e-0719
sense organ1.89e-0723
telencephalic nucleus2.18e-077
diencephalon5.44e-077
future diencephalon5.44e-077
Disease
Ontology termp-valuen
cell type cancer1.02e-12143
carcinoma1.41e-09106


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


No analysis results for this cluster

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.