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Coexpression cluster:C4573: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4573_Melanocyte_Monocytederived_Osteoblast_Alveolar_Smooth_mesothelioma_Hepatic
|full_id=C4573_Melanocyte_Monocytederived_Osteoblast_Alveolar_Smooth_mesothelioma_Hepatic
|id=C4573
|id=C4573

Revision as of 17:40, 12 September 2012


Full id: C4573_Melanocyte_Monocytederived_Osteoblast_Alveolar_Smooth_mesothelioma_Hepatic



Phase1 CAGE Peaks

Hg19::chr6:146864862..146864881,+p3@RAB32
Hg19::chr6:146864935..146864949,+p2@RAB32
Hg19::chr6:146864960..146864999,+p1@RAB32


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
somatic cell3.84e-37591
animal cell4.77e-30679
eukaryotic cell4.77e-30679
mesodermal cell3.80e-23119
granulocyte monocyte progenitor cell6.13e-2171
embryonic cell1.63e-20248
myeloid leukocyte2.25e-2076
native cell2.12e-19722
macrophage dendritic cell progenitor4.68e-1965
monopoietic cell6.88e-1963
monocyte6.88e-1963
monoblast6.88e-1963
promonocyte6.88e-1963
myeloid lineage restricted progenitor cell1.06e-1870
CD14-positive, CD16-negative classical monocyte1.83e-1842
classical monocyte1.01e-1645
contractile cell3.23e-1459
non-terminally differentiated cell5.29e-14180
smooth muscle cell2.57e-1342
smooth muscle myoblast2.57e-1342
muscle cell5.89e-1354
muscle precursor cell1.32e-1257
myoblast1.32e-1257
multi-potent skeletal muscle stem cell1.32e-1257
multi fate stem cell2.86e-12430
somatic stem cell7.51e-12436
stem cell1.96e-11444
lining cell1.27e-1057
barrier cell1.27e-1057
vascular associated smooth muscle cell2.38e-1032
myeloid cell1.27e-09112
common myeloid progenitor1.27e-09112
electrically responsive cell2.08e-0960
electrically active cell2.08e-0960
meso-epithelial cell2.74e-0944
endothelial cell5.70e-0935
columnar/cuboidal epithelial cell1.71e-0727
epithelial cell2.45e-07254
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm5.42e-34216
musculoskeletal system2.83e-30167
mesoderm7.34e-27448
mesoderm-derived structure7.34e-27448
presumptive mesoderm7.34e-27448
bone marrow7.66e-2180
bone element3.76e-1986
skeletal element3.82e-19101
skeletal system3.82e-19101
immune system1.69e-18115
epithelial tube1.07e-15118
vasculature3.74e-1579
vascular system3.74e-1579
trunk mesenchyme5.26e-15143
hemolymphoid system9.38e-15112
anatomical system9.66e-15625
anatomical group2.26e-14626
hematopoietic system6.11e-14102
blood island6.11e-14102
cardiovascular system7.25e-14110
splanchnic layer of lateral plate mesoderm1.04e-1384
somite6.10e-1383
paraxial mesoderm6.10e-1383
presomitic mesoderm6.10e-1383
presumptive segmental plate6.10e-1383
trunk paraxial mesoderm6.10e-1383
presumptive paraxial mesoderm6.10e-1383
vessel7.91e-1369
circulatory system8.03e-13113
multi-cellular organism1.94e-12659
germ layer2.30e-12604
embryonic tissue2.30e-12604
presumptive structure2.30e-12604
epiblast (generic)2.30e-12604
embryonic structure2.54e-12605
developing anatomical structure2.54e-12605
blood vessel2.63e-1260
epithelial tube open at both ends2.63e-1260
blood vasculature2.63e-1260
vascular cord2.63e-1260
dermomyotome4.08e-1270
multilaminar epithelium5.59e-1282
unilaminar epithelium6.07e-12138
artery1.65e-1142
arterial blood vessel1.65e-1142
arterial system1.65e-1142
embryo2.82e-11612
skeletal muscle tissue1.02e-1061
striated muscle tissue1.02e-1061
myotome1.02e-1061
muscle tissue4.12e-1063
musculature4.12e-1063
musculature of body4.12e-1063
trunk3.08e-08216
systemic artery3.38e-0833
systemic arterial system3.38e-0833


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
CCNT2#90536.336201576962630.003930750035764890.0190967857368586
CTCF#1066435.360256373075030.0064925092527670.0281077422421544
CTCFL#140690319.74647435897440.0001298372005551160.00172256953617579
E2F1#186934.907389214879320.008460985347239390.0327377315011979
E2F6#187635.017155731697390.00791769806886330.0324026829394206
ELF1#199734.258097958807540.01295179875054610.0464596568678785
GABPB1#255337.067683836182170.002832212825417420.0154727977859377
HMGN3#932438.178547723350590.001827766942164210.0109105024961527
HNF4A#3172323.13229036295378.07584663437677e-050.00123345034607733
RAD21#5885310.35503389545630.0009004912073565420.00667990632893741
SMC3#9126315.04493284493280.0002935825420371870.00310590225970641
SPI1#668838.204323508522730.001810593189410520.0109373903701108
TAF7#6879311.43306940492390.0006690181981945830.00545275414400219
USF1#739136.361499277207960.00388404057290560.0191035750868272
ZBTB7A#5134137.35190930787590.002516255860282270.0140795738436657



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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