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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1181_Myoblast_CD14_liposarcoma_mesenchymal_caudate_diencephalon_putamen
|full_id=C1181_Myoblast_CD14_liposarcoma_mesenchymal_caudate_diencephalon_putamen
|id=C1181
|id=C1181

Revision as of 13:40, 12 September 2012


Full id: C1181_Myoblast_CD14_liposarcoma_mesenchymal_caudate_diencephalon_putamen



Phase1 CAGE Peaks

Hg19::chr12:90102690..90102701,-p13@ATP2B1
Hg19::chr12:90102773..90102784,-p6@ATP2B1
Hg19::chr12:90102800..90102814,-p4@ATP2B1
Hg19::chr12:90102818..90102829,-p10@ATP2B1
Hg19::chr12:90102935..90102948,-p5@ATP2B1
Hg19::chr12:90102960..90102971,-p7@ATP2B1
Hg19::chr12:90102986..90102998,-p12@ATP2B1


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
CD14-positive, CD16-negative classical monocyte3.85e-2542
leukocyte1.07e-23140
classical monocyte1.23e-2345
nongranular leukocyte1.76e-20119
myeloid leukocyte2.18e-2076
macrophage dendritic cell progenitor6.82e-1965
monopoietic cell2.55e-1863
monocyte2.55e-1863
monoblast2.55e-1863
promonocyte2.55e-1863
hematopoietic lineage restricted progenitor cell6.51e-18124
granulocyte monocyte progenitor cell7.95e-1871
myeloid lineage restricted progenitor cell2.59e-1570
hematopoietic stem cell3.03e-14172
angioblastic mesenchymal cell3.03e-14172
hematopoietic oligopotent progenitor cell2.81e-13165
hematopoietic multipotent progenitor cell2.81e-13165
hematopoietic cell1.17e-11182
connective tissue cell2.97e-10365
myeloid cell4.29e-10112
common myeloid progenitor4.29e-10112
mesenchymal cell6.06e-10358
multi fate stem cell4.32e-09430
stem cell1.71e-08444
somatic stem cell3.44e-08436
motile cell2.92e-07390
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.60e-16102
blood island2.60e-16102
bone marrow1.98e-1580
bone element2.66e-1386
cerebral hemisphere3.10e-1332
regional part of forebrain8.86e-1341
forebrain8.86e-1341
future forebrain8.86e-1341
hemolymphoid system1.49e-12112
telencephalon3.94e-1234
skeletal element4.82e-12101
skeletal system4.82e-12101
regional part of cerebral cortex4.94e-1222
anterior neural tube7.76e-1242
regional part of telencephalon1.41e-1133
gray matter3.60e-1134
brain grey matter3.60e-1134
neocortex4.68e-1120
connective tissue5.49e-11375
cerebral cortex1.37e-0925
pallium1.37e-0925
neural tube2.62e-0957
neural rod2.62e-0957
future spinal cord2.62e-0957
neural keel2.62e-0957
immune system6.61e-09115
central nervous system9.96e-0982
regional part of brain1.01e-0859
brain3.06e-0869
future brain3.06e-0869
musculoskeletal system5.23e-08167
regional part of nervous system5.73e-0894
nervous system5.73e-0894


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
ATF3#467619.25414959372185.23155102976118e-083.33360560095929e-06
BHLHE40#8553744.87181354697742.71655591272133e-123.64203315749298e-10
CCNT2#90576.336201576962632.43743907326287e-068.61759307286733e-05
CHD2#1106710.34402283411697.88338195961115e-084.72094339724673e-06
CTCF#1066475.360256373075037.86114662284756e-060.00022237548541267
E2F1#186974.907389214879321.45832274679793e-050.000346779984865276
E2F6#187675.017155731697391.24910426162553e-050.000308113367926095
EGR1#195874.988179094810141.30079520165561e-050.000318084172478834
GATA1#262335.811560633057330.01119311600820290.0411271405425239
HDAC2#3066611.49910305996541.1228817392662e-064.62067162991419e-05
HEY1#2346274.040111043105715.68979821988558e-050.00094986706567556
JUND#372765.995426235889455.24232039014691e-050.000891262736816789
MAX#414965.530761864863258.40673768319711e-050.00126184431861946
NFKB1#479075.488063424193846.66568321176054e-060.000194674857089782
NRF1#489958.721628176936366.71450045004423e-050.00107356967621275
PAX5#507976.669565531177831.7023051190758e-066.43456548429814e-05
POLR2A#543072.147453176558070.004747636447610280.0223330512094392
SIN3A#2594275.408884726815147.3795239773719e-060.000211559183275527
TAF1#687273.343046285745290.0002142336319622450.00246522105426454
TBP#690863.177232017511190.002074112051852660.012018986216692
TFAP2C#7022710.80922860986025.79365976833206e-083.61028659036296e-06
USF1#739165.452713666178259.13505145927422e-050.00133136427484669
USF2#7392712.99219738506961.59819543071901e-081.16641462326249e-06



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.