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Coexpression cluster:C1030: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;6:3.68054191115949:0.00136649155081914:0.0089921877056266!ZNF263#10127;6:6.16638122775801:7.27120729623729e-05:0.00114246670499733
|tf_chipseq_enrich=E2F1#1869;6:3.68054191115949:0.00136649155081914:0.0089921877056266!ZNF263#10127;6:6.16638122775801:7.27120729623729e-05:0.00114246670499733
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.898711,0.341646,0.481684,0.301904,1.20684,0.554663,0.19223,0.555925,2.43082,0.450635,0.597407,0.152895,0.543352,0.81316,0.863056,0.774423,0.250594,0.163559,0.0766963,0.341703,0.047825,0.472508,0.29709,0.385586,0.619829,0.833436,0.470396,3.14801,0.388322,0.429397,0.810962,0.220667,0.154814,0.269459,2.02711,7.9481,1.20926,1.27056,0.174436,0.268162,1.06332,0.0547276,0.299183,0.949078,0.371118,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,1.4101,0.712797,1.12756,1.49516,0.800646,1.33315,2.73679,0.573519,4.21368,1.03748,0.149081,2.6554,0.127753,2.90352,0.797419,0.989108,0.167664,0.745864,0.575394,0.19474,0.986227,2.4135,7.9978,2.45026,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,1.48306,0.239285,3.67624,0.87,0.664183,0.106284,2.76279,0.822041,0.864454,0.778061,0.701386,1.13403,0.762347,0.539961,0.385342,1.42617,0.92894,0.861701,0.893372,0.459808,1.17281,0.265019,1.199,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,1.25306,0.960022,0.432175,1.08604,0.583225,1.23359,1.20791,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,2.32574,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,2.61346,0.593875,1.14002,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,2.5479,0.71907,0.574616,0.611402,0.553354,0.0203307
}}
}}

Revision as of 14:38, 26 November 2012


Full id: C1030_Astrocyte_anaplastic_Neural_parietal_hippocampus_occipital_spinal



Phase1 CAGE Peaks

Hg19::chr14:33403589..33403617,+p@chr14:33403589..33403617
+
Hg19::chr14:33403648..33403710,+p3@NPAS3
Hg19::chr14:33403779..33403793,+p6@NPAS3
Hg19::chr14:33403860..33403874,+p5@NPAS3
Hg19::chr14:33403881..33403924,+p1@NPAS3
Hg19::chr14:33403930..33403943,+p7@NPAS3
Hg19::chr14:33705034..33705038,+p@chr14:33705034..33705038
+
Hg19::chr9:14317049..14317093,+p1@ENST00000416996


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><br>

Cell Type
Ontology termp-valuen
neural cell4.54e-1125
oligodendrocyte3.87e-087
macroglial cell3.87e-087
astrocyte3.87e-087
oligodendrocyte precursor cell3.87e-087
neuronal stem cell5.79e-078
Uber Anatomy
Ontology termp-valuen
central nervous system1.12e-7781
neural tube1.71e-7256
neural rod1.71e-7256
future spinal cord1.71e-7256
neural keel1.71e-7256
nervous system6.42e-7089
regional part of nervous system1.14e-6753
regional part of brain1.14e-6753
brain2.50e-6468
future brain2.50e-6468
neural plate5.08e-5982
presumptive neural plate5.08e-5982
neurectoderm2.39e-5786
regional part of forebrain1.68e-5341
forebrain1.68e-5341
anterior neural tube1.68e-5341
future forebrain1.68e-5341
brain grey matter4.03e-5034
gray matter4.03e-5034
telencephalon7.10e-5034
cerebral hemisphere4.38e-4732
regional part of telencephalon5.13e-4732
ecto-epithelium1.41e-45104
pre-chordal neural plate1.01e-4461
ectoderm-derived structure4.12e-42171
ectoderm4.12e-42171
presumptive ectoderm4.12e-42171
adult organism2.36e-40114
structure with developmental contribution from neural crest4.82e-37132
cerebral cortex8.46e-3725
pallium8.46e-3725
regional part of cerebral cortex8.83e-3222
neocortex1.43e-2820
organ system subdivision3.25e-28223
posterior neural tube3.24e-1915
chordal neural plate3.24e-1915
anatomical cluster3.04e-17373
segmental subdivision of hindbrain8.83e-1512
hindbrain8.83e-1512
presumptive hindbrain8.83e-1512
neural nucleus1.59e-149
nucleus of brain1.59e-149
basal ganglion1.80e-149
nuclear complex of neuraxis1.80e-149
aggregate regional part of brain1.80e-149
collection of basal ganglia1.80e-149
cerebral subcortex1.80e-149
segmental subdivision of nervous system2.09e-1313
tube2.50e-12192
epithelium3.75e-12306
cell layer7.86e-12309
telencephalic nucleus1.51e-117
organ part3.62e-11218
multi-tissue structure3.85e-11342
regional part of metencephalon1.46e-109
metencephalon1.46e-109
future metencephalon1.46e-109
brainstem3.52e-106
gyrus3.57e-106
anatomical conduit1.17e-09240
embryo1.57e-09592
limbic system3.32e-095
occipital lobe6.57e-095
developing anatomical structure7.30e-09581
temporal lobe8.95e-096
parietal lobe1.08e-085
embryonic structure1.20e-08564
germ layer1.94e-08560
germ layer / neural crest1.94e-08560
embryonic tissue1.94e-08560
presumptive structure1.94e-08560
germ layer / neural crest derived structure1.94e-08560
epiblast (generic)1.94e-08560
multi-cellular organism3.90e-08656
organ4.48e-08503
corpus striatum2.00e-074
striatum2.00e-074
ventral part of telencephalon2.00e-074
future corpus striatum2.00e-074
anatomical system5.29e-07624
anatomical group6.04e-07625
regional part of diencephalon7.40e-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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186963.680541911159490.001366491550819140.0089921877056266
ZNF263#1012766.166381227758017.27120729623729e-050.00114246670499733



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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