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Coexpression cluster:C3171: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,2.0185,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,1.11965,0.599922,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,1.32383,0.63803,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,0.936473,0.56135
}}
}}

Revision as of 15:58, 26 November 2012


Full id: C3171_optic_thalamus_Mesothelial_diencephalon_Retinal_spinal_occipital



Phase1 CAGE Peaks

Hg19::chr11:61536730..61536771,+p@chr11:61536730..61536771
+
Hg19::chr11:61537818..61537845,+p@chr11:61537818..61537845
+
Hg19::chr11:61538994..61539023,+p@chr11:61538994..61539023
+


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

No GOStat results

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>disease_data<br>

Cell Type
Ontology termp-valuen
mesothelial cell4.98e-0919
Uber Anatomy
Ontology termp-valuen
neural tube3.36e-3156
neural rod3.36e-3156
future spinal cord3.36e-3156
neural keel3.36e-3156
brain2.87e-2968
future brain2.87e-2968
regional part of nervous system6.08e-2853
regional part of brain6.08e-2853
central nervous system1.35e-2781
neural plate4.48e-2582
presumptive neural plate4.48e-2582
nervous system1.46e-2489
neurectoderm3.77e-2486
regional part of forebrain2.34e-2041
forebrain2.34e-2041
anterior neural tube2.34e-2041
future forebrain2.34e-2041
adult organism2.48e-20114
brain grey matter2.86e-2034
gray matter2.86e-2034
telencephalon4.55e-2034
tube6.41e-20192
regional part of telencephalon4.27e-1832
cerebral hemisphere8.92e-1832
pre-chordal neural plate2.41e-1761
organ system subdivision8.75e-17223
structure with developmental contribution from neural crest2.46e-16132
ecto-epithelium2.50e-16104
anatomical conduit1.46e-13240
regional part of cerebral cortex2.49e-1222
cell layer2.52e-12309
posterior neural tube3.10e-1215
chordal neural plate3.10e-1215
neocortex4.34e-1220
anatomical cluster7.63e-12373
multi-tissue structure1.11e-11342
neural nucleus1.67e-119
nucleus of brain1.67e-119
cerebral cortex1.80e-1125
pallium1.80e-1125
epithelium2.41e-11306
segmental subdivision of nervous system3.79e-1013
epithelium of foregut-midgut junction1.68e-0925
anatomical boundary1.68e-0925
hepatobiliary system1.68e-0925
foregut-midgut junction1.68e-0925
septum transversum1.68e-0925
ectoderm-derived structure1.72e-09171
ectoderm1.72e-09171
presumptive ectoderm1.72e-09171
telencephalic nucleus4.27e-097
segmental subdivision of hindbrain6.36e-0912
hindbrain6.36e-0912
presumptive hindbrain6.36e-0912
brainstem9.73e-096
basal ganglion1.21e-089
nuclear complex of neuraxis1.21e-089
aggregate regional part of brain1.21e-089
collection of basal ganglia1.21e-089
cerebral subcortex1.21e-089
hepatic diverticulum1.50e-0822
liver primordium1.50e-0822
epithelial sac2.90e-0825
abdomen element4.02e-0854
abdominal segment element4.02e-0854
digestive tract diverticulum5.28e-0823
sac8.84e-0826
occipital lobe6.77e-075
Disease
Ontology termp-valuen
ovarian cancer4.92e-0814


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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