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Coexpression cluster:C4864: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191484492273543!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663434856528923!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00439563239153496!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324892530494269!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322986282515139!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00389834557476722!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00439518163042606!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109380100660491!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128887495648456!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00200393413735867!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246901785972537!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00137493912519777!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0248222923254659!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000943375266938726!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109500574502777!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376797523153773!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00546469510411732!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0141120849421125
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191484492273543!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663434856528923!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00439563239153496!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324892530494269!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322986282515139!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00389834557476722!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00439518163042606!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109380100660491!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128887495648456!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00200393413735867!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246901785972537!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00137493912519777!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0248222923254659!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000943375266938726!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109500574502777!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376797523153773!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00546469510411732!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0141120849421125
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}}
}}

Revision as of 17:00, 26 November 2012


Full id: C4864_Mast_CD14_Eosinophils_Monocytederived_chronic_Reticulocytes_Macrophage



Phase1 CAGE Peaks

Hg19::chrX:154033633..154033644,-p4@MPP1
Hg19::chrX:154033645..154033656,-p3@MPP1
Hg19::chrX:154033661..154033676,-p2@MPP1


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>


Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm5.77e-23203
hemolymphoid system2.57e-22108
adult organism9.54e-21114
hematopoietic system1.20e-2098
blood island1.20e-2098
immune system7.11e-2093
bone marrow1.59e-1976
mesoderm5.55e-18315
mesoderm-derived structure5.55e-18315
presumptive mesoderm5.55e-18315
bone element1.07e-1782
musculoskeletal system1.44e-14167
skeletal element2.57e-1490
skeletal system8.61e-13100
anatomical system6.71e-10624
circulatory system9.28e-10112
anatomical group1.24e-09625
multi-cellular organism1.49e-09656
cardiovascular system4.53e-09109
tissue1.26e-08773
germ layer1.55e-08560
germ layer / neural crest1.55e-08560
embryonic tissue1.55e-08560
presumptive structure1.55e-08560
germ layer / neural crest derived structure1.55e-08560
epiblast (generic)1.55e-08560
embryonic structure3.83e-08564
developing anatomical structure8.65e-08581
neural tube1.96e-0756
neural rod1.96e-0756
future spinal cord1.96e-0756
neural keel1.96e-0756
regional part of nervous system2.68e-0753
regional part of brain2.68e-0753
organ3.61e-07503
embryo4.84e-07592
tube4.98e-07192
anatomical conduit8.97e-07240


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#90536.336201576962630.003930750035764890.0191484492273543
CHD2#1106310.34402283411690.0009033701102746880.00663434856528923
E2F4#1874312.66806031528440.0004917987006298980.00439563239153496
E2F6#187635.017155731697390.00791769806886330.0324892530494269
EGR1#195834.988179094810140.008056488137383440.0322986282515139
GATA1#2623313.56030814380040.0004009615963782630.00389834557476722
GATA2#2624312.7449317335540.0004829527704283790.00439518163042606
HMGN3#932438.178547723350590.001827766942164210.0109380100660491
IRF1#365937.63716375356390.002244692747297240.0128887495648456
NFYA#4800318.42558069983050.0001598135507814160.00200393413735867
NFYB#4801316.75979325353650.0002123649923296180.00246901785972537
PBX3#5090321.91451268674419.49854535978121e-050.00137493912519777
SP1#666735.69838137814090.005403962701712170.0248222923254659
SP2#6668326.15353049384465.58768218891694e-050.000943375266938726
SPI1#668838.204323508522730.001810593189410520.0109500574502777
SRF#6722313.79717826216780.0003806615025800190.00376797523153773
TAF7#6879311.43306940492390.0006690181981945830.00546469510411732
ZBTB7A#5134137.35190930787590.002516255860282270.0141120849421125



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.