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Coexpression cluster:C751: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!2.15e-67!114;UBERON:0001049!2.07e-55!56;UBERON:0005068!2.07e-55!56;UBERON:0006241!2.07e-55!56;UBERON:0007135!2.07e-55!56;UBERON:0000073!5.67e-52!53;UBERON:0002616!5.67e-52!53;UBERON:0003075!2.59e-51!82;UBERON:0007284!2.59e-51!82;UBERON:0001017!2.53e-49!81;UBERON:0002346!6.18e-48!86;UBERON:0001016!1.23e-45!89;UBERON:0002780!1.13e-43!41;UBERON:0001890!1.13e-43!41;UBERON:0003080!1.13e-43!41;UBERON:0006240!1.13e-43!41;UBERON:0000955!1.22e-43!68;UBERON:0006238!1.22e-43!68;UBERON:0010371!3.14e-43!104;UBERON:0003056!4.23e-38!61;UBERON:0010314!5.11e-36!132;UBERON:0003528!1.06e-34!34;UBERON:0002020!1.06e-34!34;UBERON:0001893!1.14e-34!34;UBERON:0001869!1.22e-32!32;UBERON:0002791!3.70e-32!32;UBERON:0004121!1.61e-29!171;UBERON:0000924!1.61e-29!171;UBERON:0006601!1.61e-29!171;UBERON:0002619!6.02e-28!22;UBERON:0001950!2.59e-25!20;UBERON:0000956!8.77e-24!25;UBERON:0000203!8.77e-24!25;UBERON:0011216!7.00e-20!223;UBERON:0000477!1.45e-17!373;UBERON:0000025!7.33e-15!192;UBERON:0004111!2.22e-13!240;UBERON:0000062!1.21e-12!503;UBERON:0002420!1.26e-12!9;UBERON:0007245!1.26e-12!9;UBERON:0010009!1.26e-12!9;UBERON:0010011!1.26e-12!9;UBERON:0000454!1.26e-12!9;UBERON:0003076!1.36e-12!15;UBERON:0003057!1.36e-12!15;UBERON:0000125!1.80e-12!9;UBERON:0002308!1.80e-12!9;UBERON:0000481!1.09e-11!342;UBERON:0000922!1.03e-10!592;UBERON:0000483!1.88e-10!306;UBERON:0001894!2.09e-10!7;UBERON:0006222!2.09e-10!7;UBERON:0000064!2.32e-10!218;UBERON:0000119!3.85e-10!309;UBERON:0009663!5.76e-10!7;UBERON:0000468!1.15e-09!656;UBERON:0004733!1.66e-09!12;UBERON:0002028!1.66e-09!12;UBERON:0007277!1.66e-09!12;UBERON:0002298!2.46e-09!6;UBERON:0000200!2.91e-09!6;UBERON:0005423!8.45e-09!581;UBERON:0000467!1.28e-08!624;UBERON:0004732!1.39e-08!13;UBERON:0000480!1.50e-08!625;UBERON:0000349!3.18e-08!5;UBERON:0002050!4.41e-08!564;UBERON:0001872!6.78e-08!5;UBERON:0003135!7.35e-08!11;UBERON:0002021!7.92e-08!5;UBERON:0001871!1.02e-07!6;UBERON:0000923!1.30e-07!560;UBERON:0010316!1.30e-07!560;UBERON:0005291!1.30e-07!560;UBERON:0006598!1.30e-07!560;UBERON:0010317!1.30e-07!560;UBERON:0002532!1.30e-07!560;UBERON:0000369!6.20e-07!4;UBERON:0002435!6.20e-07!4;UBERON:0000204!6.20e-07!4;UBERON:0010082!6.20e-07!4;UBERON:0003296!9.44e-07!4;UBERON:0010133!9.44e-07!4;UBERON:0002784!9.86e-07!4
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|tfbs_overrepresentation_for_novel_motifs=1.30185,1.32694,0.246925,0.373402,0.21227,0.371921,1.9648,0.384145,0.11927,4.92411,0.344881,0.481459,0.3032,0.430675,0.606477,0.230406,0.650562,0.168654,0.667607,0.14663,0.246975,0.0880531,0.36495,0.20812,0.779948,0.50266,0.95707,0.363006,0.615097,0.068246,0.325512,0.685875,0.14393,0.635939,0.184525,0.153902,0.182011,0.372963,0.163827,1.708,0.183426,0.311187,0.101961,0.209923,1.06942,0.273032,0.442265,0.335245,0.229828,0.214901,0.515974,0.453148,0.0475371,0.760015,0.908824,0.433372,0.218374,0.40339,0.88505,1.03906,1.72258,0.444449,0.119615,1.51165,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,1.47256,0.125091,0.702612,0.906867,2.72777,0.576459,0.071925,0.607953,0.672773,0.280653,0.101808,0.623044,0.46072,0.123028,0.856604,6.40134,0.0364455,0.0654897,0.540459,1.45821,1.08742,0.830286,0.702047,0.149302,0.610551,0.159241,0.322542,0.743159,0.544807,0.0567143,0.164861,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,1.09593,2.02787,0.735091,0.679564,0.353283,1.04009,0.180771,4.32544,0.324453,0.58906,0.151445,0.898765,0.538171,0.369441,0.471181,1.14929,0.608677,1.11065,0.706859,0.940494,0.482616,0.830959,0.328039,0.954592,0.468088,1.10012,1.76064,0.32024,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,0.395692,0.566218,1.75262,0.308276,0.881992,1.01851,1.06355,0.831331,0.113748,0.444001,1.22899,0.525224,0.200973,0.286011,0.723559,1.02032,0.813307,0.672017,0.729849,0.597299,0.459987,0.137885,0.440034,1.11454
}}
}}

Revision as of 14:26, 26 November 2012


Full id: C751_heart_pineal_left_cerebellum_pons_putamen_Mesothelial



Phase1 CAGE Peaks

Hg19::chr13:30079614..30079618,+p@chr13:30079614..30079618
+
Hg19::chr16:58497281..58497330,+p6@NDRG4
Hg19::chr16:58497337..58497348,+p9@NDRG4
Hg19::chr16:58497587..58497668,+p2@NDRG4
Hg19::chr16:58498177..58498193,+p4@NDRG4
Hg19::chr16:58498194..58498236,+p3@NDRG4
Hg19::chr1:62417957..62417993,+p4@INADL
Hg19::chr1:62417997..62418034,+p3@INADL
Hg19::chr2:220492344..220492368,+p1@SLC4A3
Hg19::chr2:220492373..220492391,+p2@SLC4A3
Hg19::chr5:31639211..31639288,+p1@PDZD2


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:0005911intercellular junction0.0104492723300696
GO:0030054cell junction0.0261672940711137
GO:0044459plasma membrane part0.0261672940711137
GO:0015106bicarbonate transmembrane transporter activity0.032980560816889
GO:0005452inorganic anion exchanger activity0.032980560816889
GO:0015380anion exchanger activity0.032980560816889
GO:0015301anion:anion antiporter activity0.032980560816889
GO:0015108chloride transmembrane transporter activity0.032980560816889
GO:0005886plasma membrane0.0392005153929385



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><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.15e-67114
neural tube2.07e-5556
neural rod2.07e-5556
future spinal cord2.07e-5556
neural keel2.07e-5556
regional part of nervous system5.67e-5253
regional part of brain5.67e-5253
neural plate2.59e-5182
presumptive neural plate2.59e-5182
central nervous system2.53e-4981
neurectoderm6.18e-4886
nervous system1.23e-4589
regional part of forebrain1.13e-4341
forebrain1.13e-4341
anterior neural tube1.13e-4341
future forebrain1.13e-4341
brain1.22e-4368
future brain1.22e-4368
ecto-epithelium3.14e-43104
pre-chordal neural plate4.23e-3861
structure with developmental contribution from neural crest5.11e-36132
brain grey matter1.06e-3434
gray matter1.06e-3434
telencephalon1.14e-3434
cerebral hemisphere1.22e-3232
regional part of telencephalon3.70e-3232
ectoderm-derived structure1.61e-29171
ectoderm1.61e-29171
presumptive ectoderm1.61e-29171
regional part of cerebral cortex6.02e-2822
neocortex2.59e-2520
cerebral cortex8.77e-2425
pallium8.77e-2425
organ system subdivision7.00e-20223
anatomical cluster1.45e-17373
tube7.33e-15192
anatomical conduit2.22e-13240
organ1.21e-12503
basal ganglion1.26e-129
nuclear complex of neuraxis1.26e-129
aggregate regional part of brain1.26e-129
collection of basal ganglia1.26e-129
cerebral subcortex1.26e-129
posterior neural tube1.36e-1215
chordal neural plate1.36e-1215
neural nucleus1.80e-129
nucleus of brain1.80e-129
multi-tissue structure1.09e-11342
embryo1.03e-10592
epithelium1.88e-10306
diencephalon2.09e-107
future diencephalon2.09e-107
organ part2.32e-10218
cell layer3.85e-10309
telencephalic nucleus5.76e-107
multi-cellular organism1.15e-09656
segmental subdivision of hindbrain1.66e-0912
hindbrain1.66e-0912
presumptive hindbrain1.66e-0912
brainstem2.46e-096
gyrus2.91e-096
developing anatomical structure8.45e-09581
anatomical system1.28e-08624
segmental subdivision of nervous system1.39e-0813
anatomical group1.50e-08625
limbic system3.18e-085
embryonic structure4.41e-08564
parietal lobe6.78e-085
male reproductive organ7.35e-0811
occipital lobe7.92e-085
temporal lobe1.02e-076
germ layer1.30e-07560
germ layer / neural crest1.30e-07560
embryonic tissue1.30e-07560
presumptive structure1.30e-07560
germ layer / neural crest derived structure1.30e-07560
epiblast (generic)1.30e-07560
corpus striatum6.20e-074
striatum6.20e-074
ventral part of telencephalon6.20e-074
future corpus striatum6.20e-074
gland of diencephalon9.44e-074
neuroendocrine gland9.44e-074
regional part of diencephalon9.86e-074


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.

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