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Coexpression cluster:C3173: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3173_CD4_CD14_CD8_Natural_Peripheral_Chondrocyte_CD19
|full_id=C3173_CD4_CD14_CD8_Natural_Peripheral_Chondrocyte_CD19
|id=C3173
|id=C3173

Revision as of 16:02, 12 September 2012


Full id: C3173_CD4_CD14_CD8_Natural_Peripheral_Chondrocyte_CD19



Phase1 CAGE Peaks

Hg19::chr11:62608867..62608952,-p@chr11:62608867..62608952
-
Hg19::chr16:3314414..3314469,-p@chr16:3314414..3314469
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Hg19::chr18:3449633..3449649,-p@chr18:3449633..3449649
-


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
leukocyte8.77e-31140
hematopoietic lineage restricted progenitor cell5.76e-27124
nongranular leukocyte3.76e-26119
hematopoietic stem cell6.25e-25172
angioblastic mesenchymal cell6.25e-25172
hematopoietic cell2.47e-23182
hematopoietic oligopotent progenitor cell2.30e-22165
hematopoietic multipotent progenitor cell2.30e-22165
classical monocyte3.15e-2245
CD14-positive, CD16-negative classical monocyte6.39e-2242
lymphoid lineage restricted progenitor cell3.47e-1652
lymphocyte4.55e-1653
common lymphoid progenitor4.55e-1653
myeloid leukocyte1.12e-1276
mature alpha-beta T cell1.80e-1118
alpha-beta T cell1.80e-1118
immature T cell1.80e-1118
mature T cell1.80e-1118
immature alpha-beta T cell1.80e-1118
myeloid lineage restricted progenitor cell6.23e-1170
T cell8.45e-1125
pro-T cell8.45e-1125
granulocyte monocyte progenitor cell2.37e-1071
macrophage dendritic cell progenitor3.81e-1065
monopoietic cell1.41e-0963
monocyte1.41e-0963
monoblast1.41e-0963
promonocyte1.41e-0963
myeloid cell1.18e-08112
common myeloid progenitor1.18e-08112
mesenchymal cell2.89e-07358
CD8-positive, alpha-beta T cell3.14e-0711
connective tissue cell6.42e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.26e-13102
blood island2.26e-13102
hemolymphoid system2.44e-11112
bone element3.24e-1086
bone marrow3.99e-1080
skeletal element3.54e-09101
skeletal system3.54e-09101
connective tissue8.85e-07375


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
BRF2#552901358.1918604651160.002789217733358720.0152754646488857
E2F6#187635.017155731697390.00791769806886330.0320572385584033
ELF1#199734.258097958807540.01295179875054610.0460218055834337
ESRRA#21011161.2801047120420.006187620080219560.0273466570842559
IRF4#3662214.60967512449610.006056122473217890.0268097395295186
KAT2A#26481205.3633333333330.004861545220737780.0227520577750777
MAX#414936.452555509007120.003721913834265510.018583590330203
MEF2A#4205212.4954872730960.008235029478029740.0324746353895162
MYC#460935.22228187160940.007020843755740150.0293276498282436
PBX3#5090214.60967512449610.006056122473217890.0268108759688188
POU5F1#54601111.8130671506350.008916911055111830.0338202089513664
PPARGC1A#108911116.6837121212120.008545763211786680.0325626970730705
SETDB1#9869226.8800174520070.001814468907964410.010890880360856
SIN3A#2594235.408884726815140.006318961977991520.0275528586347469
SMC3#9126210.02995522995520.0126656379767470.0457142163620915
SP2#6668217.43568699589640.004273568481769740.0203088328100992
SREBF2#67211145.6477541371160.006850215514569990.0290435455740744
STAT1#6772213.80439166479950.006770931708444080.0287447395105155
TCF7L2#6934310.77017656313730.0008003181298398380.00611891838670153
TFAP2A#7020211.01242291536330.01054990655215560.0389942557474725
XRCC4#751811432.767441860460.0006977913838891460.00561193857554278



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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