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Coexpression cluster:C3277: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.94e-36!115;UBERON:0001049!4.37e-35!57;UBERON:0005068!4.37e-35!57;UBERON:0006241!4.37e-35!57;UBERON:0007135!4.37e-35!57;UBERON:0002616!1.56e-31!59;UBERON:0005743!4.71e-31!86;UBERON:0000955!4.78e-30!69;UBERON:0006238!4.78e-30!69;UBERON:0001017!8.98e-30!82;UBERON:0000073!1.34e-27!94;UBERON:0001016!1.34e-27!94;UBERON:0003080!5.92e-27!42;UBERON:0002780!2.95e-26!41;UBERON:0001890!2.95e-26!41;UBERON:0006240!2.95e-26!41;UBERON:0002390!2.65e-25!102;UBERON:0003061!2.65e-25!102;UBERON:0003075!6.72e-23!86;UBERON:0007284!6.72e-23!86;UBERON:0002371!2.28e-22!80;UBERON:0001893!3.27e-22!34;UBERON:0002020!4.48e-22!34;UBERON:0003528!4.48e-22!34;UBERON:0002405!2.55e-21!115;UBERON:0002193!2.95e-21!112;UBERON:0002791!3.81e-21!33;UBERON:0002346!4.18e-21!90;UBERON:0001869!4.07e-20!32;UBERON:0001474!1.17e-19!86;UBERON:0003056!7.26e-18!61;UBERON:0002619!1.01e-16!22;UBERON:0004765!3.32e-16!101;UBERON:0001434!3.32e-16!101;UBERON:0000062!5.49e-15!511;UBERON:0001950!8.43e-15!20;UBERON:0000956!5.43e-14!25;UBERON:0000203!5.43e-14!25;UBERON:0000033!3.71e-13!123;UBERON:0000153!6.74e-13!129;UBERON:0007811!6.74e-13!129;UBERON:0002308!4.68e-10!9;UBERON:0000125!4.68e-10!9;UBERON:0000923!9.66e-10!604;UBERON:0005291!9.66e-10!604;UBERON:0006598!9.66e-10!604;UBERON:0002532!9.66e-10!604;UBERON:0002050!1.18e-09!605;UBERON:0005423!1.18e-09!605;UBERON:0003076!3.55e-09!15;UBERON:0003057!3.55e-09!15;UBERON:0000922!4.62e-09!612;UBERON:0000467!9.16e-09!625;UBERON:0000480!1.11e-08!626;UBERON:0004732!3.31e-08!13;UBERON:0004121!4.37e-08!169;UBERON:0000200!4.63e-08!6;UBERON:0009663!5.63e-08!7;UBERON:0002420!8.69e-08!9;UBERON:0007245!8.69e-08!9;UBERON:0010009!8.69e-08!9;UBERON:0010011!8.69e-08!9;UBERON:0000454!8.69e-08!9;UBERON:0000924!1.47e-07!173;UBERON:0006601!1.47e-07!173;UBERON:0002298!1.86e-07!8;UBERON:0004733!3.06e-07!12;UBERON:0002028!3.06e-07!12;UBERON:0007277!3.06e-07!12;UBERON:0001872!6.56e-07!5;UBERON:0000468!6.78e-07!659
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}}
}}

Revision as of 19:02, 8 August 2012


Full id: C3277_Pericytes_kidney_Hepatocyte_endometrial_liver_Monocytederived_brain



Phase1 CAGE Peaks

Hg19::chr12:323187..323209,-p3@SLC6A12
Hg19::chr12:323248..323263,-p4@SLC6A12
Hg19::chr12:323312..323329,-p2@SLC6A12


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
macrophage dendritic cell progenitor3.06e-3065
monopoietic cell2.68e-2863
monocyte2.68e-2863
monoblast2.68e-2863
promonocyte2.68e-2863
granulocyte monocyte progenitor cell2.36e-2771
myeloid leukocyte8.70e-2776
CD14-positive, CD16-negative classical monocyte2.95e-2642
classical monocyte6.34e-2545
myeloid lineage restricted progenitor cell6.50e-2570
myeloid cell1.94e-17112
common myeloid progenitor1.94e-17112
leukocyte5.18e-13140
nongranular leukocyte1.92e-10119
hematopoietic lineage restricted progenitor cell4.09e-10124
intermediate monocyte4.65e-099
CD14-positive, CD16-positive monocyte4.65e-099
conventional dendritic cell5.07e-088
hematopoietic stem cell1.34e-07172
angioblastic mesenchymal cell1.34e-07172
hematopoietic oligopotent progenitor cell1.43e-07165
hematopoietic multipotent progenitor cell1.43e-07165
hematopoietic cell1.88e-07182
Langerhans cell9.29e-075
Uber Anatomy
Ontology termp-valuen
adult organism4.94e-36115
neural tube4.37e-3557
neural rod4.37e-3557
future spinal cord4.37e-3557
neural keel4.37e-3557
regional part of brain1.56e-3159
brain4.78e-3069
future brain4.78e-3069
central nervous system8.98e-3082
regional part of nervous system1.34e-2794
nervous system1.34e-2794
anterior neural tube5.92e-2742
regional part of forebrain2.95e-2641
forebrain2.95e-2641
future forebrain2.95e-2641
hematopoietic system2.65e-25102
blood island2.65e-25102
neural plate6.72e-2386
presumptive neural plate6.72e-2386
bone marrow2.28e-2280
telencephalon3.27e-2234
gray matter4.48e-2234
brain grey matter4.48e-2234
immune system2.55e-21115
hemolymphoid system2.95e-21112
regional part of telencephalon3.81e-2133
neurectoderm4.18e-2190
cerebral hemisphere4.07e-2032
bone element1.17e-1986
pre-chordal neural plate7.26e-1861
regional part of cerebral cortex1.01e-1622
skeletal element3.32e-16101
skeletal system3.32e-16101
organ5.49e-15511
neocortex8.43e-1520
cerebral cortex5.43e-1425
pallium5.43e-1425
head3.71e-13123
anterior region of body6.74e-13129
craniocervical region6.74e-13129
nucleus of brain4.68e-109
neural nucleus4.68e-109
germ layer9.66e-10604
embryonic tissue9.66e-10604
presumptive structure9.66e-10604
epiblast (generic)9.66e-10604
embryonic structure1.18e-09605
developing anatomical structure1.18e-09605
posterior neural tube3.55e-0915
chordal neural plate3.55e-0915
embryo4.62e-09612
anatomical system9.16e-09625
anatomical group1.11e-08626
segmental subdivision of nervous system3.31e-0813
ectoderm-derived structure4.37e-08169
gyrus4.63e-086
telencephalic nucleus5.63e-087
basal ganglion8.69e-089
nuclear complex of neuraxis8.69e-089
aggregate regional part of brain8.69e-089
collection of basal ganglia8.69e-089
cerebral subcortex8.69e-089
ectoderm1.47e-07173
presumptive ectoderm1.47e-07173
brainstem1.86e-078
segmental subdivision of hindbrain3.06e-0712
hindbrain3.06e-0712
presumptive hindbrain3.06e-0712
parietal lobe6.56e-075
multi-cellular organism6.78e-07659


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.