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Coexpression cluster:C2815: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513267011747912!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268512515907826!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129300199036826!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998648929536017!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101614667182627!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161212895130241!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195321768003361!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390768711218126!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186498743755422!HNF4G#3174;2:14.3767112632234:0.00692416998043918:0.0293106918201641!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00308009004021692!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486130057735469!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142665578824367!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00889328744744976!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.00023503538817258!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.00031181200538442!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444759107869079!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188656701145539!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.00082793415977406!RXRA#6256;3:15.05596285435:0.000475830799730358:0.00433982122897903!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797716462044075!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00685460890682043!SP2#6668;4:26.1535304938446:2.13562021071447e-06:7.7606833398333e-05!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249763804539605!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123388824518214!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323081895110129!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244875117357237!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115675292002037!THAP1#55145;4:31.3691446028513:1.03171810326891e-06:4.32390076193025e-05!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508778555310301!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00347173232595726!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.0003050063252712
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}}
}}

Revision as of 15:44, 26 November 2012


Full id: C2815_Monocytederived_CD14_Mast_corpus_Macrophage_Dendritic_optic



Phase1 CAGE Peaks

Hg19::chr5:150632645..150632658,+p5@GM2A
Hg19::chr5:150632666..150632677,+p6@GM2A
Hg19::chr5:150632678..150632707,+p3@GM2A
Hg19::chr5:150632712..150632725,+p4@GM2A


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
organ2.99e-16503
neural tube2.73e-1556
neural rod2.73e-1556
future spinal cord2.73e-1556
neural keel2.73e-1556
anatomical group1.53e-14625
anatomical system2.71e-14624
neural plate5.74e-1482
presumptive neural plate5.74e-1482
regional part of nervous system1.08e-1353
regional part of brain1.08e-1353
adult organism1.42e-13114
ecto-epithelium1.57e-13104
multi-cellular organism3.70e-13656
central nervous system4.83e-1281
neurectoderm1.37e-1186
embryonic structure1.65e-11564
brain2.62e-1168
future brain2.62e-1168
germ layer3.06e-11560
germ layer / neural crest3.06e-11560
embryonic tissue3.06e-11560
presumptive structure3.06e-11560
germ layer / neural crest derived structure3.06e-11560
epiblast (generic)3.06e-11560
regional part of forebrain1.37e-1041
forebrain1.37e-1041
anterior neural tube1.37e-1041
future forebrain1.37e-1041
developing anatomical structure1.55e-10581
bone marrow2.80e-1076
pre-chordal neural plate6.78e-1061
bone element8.89e-1082
skeletal element9.58e-1090
embryo9.63e-10592
telencephalon1.02e-0934
brain grey matter1.38e-0934
gray matter1.38e-0934
nervous system1.41e-0989
immune system1.56e-0993
structure with developmental contribution from neural crest2.90e-09132
ectoderm-derived structure3.40e-09171
ectoderm3.40e-09171
presumptive ectoderm3.40e-09171
skeletal system5.03e-09100
regional part of telencephalon1.09e-0832
cerebral hemisphere1.21e-0832
tissue2.73e-07773


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#90546.336201576962630.0006203100587215640.00513267011747912
CEBPB#105147.971147625824820.0002476385788090830.00268512515907826
CHD2#1106410.34402283411698.73193255208051e-050.00129300199036826
E2F6#187645.017155731697390.00157802193473060.00998648929536017
EGR1#195844.988179094810140.001615011500076050.0101614667182627
ELF1#199744.258097958807540.003041525565781240.0161212895130241
FOS#235348.99795530889440.0001525147711168630.00195321768003361
GABPB1#255347.067683836182170.0004006876864423170.00390768711218126
HEY1#2346244.040111043105710.00375304636917980.0186498743755422
HNF4G#3174214.37671126322340.006924169980439180.0293106918201641
IRF1#365947.63716375356390.0002938853996185490.00308009004021692
MAX#414946.452555509007120.0005767613195645490.00486130057735469
MXI1#460149.96157162875930.0001015224754950450.00142665578824367
MYC#460945.22228187160940.001344309395272740.00889328744744976
NFYA#4800418.42558069983058.67100748407158e-060.00023503538817258
NFYB#4801416.75979325353651.26678572070404e-050.00031181200538442
PAX5#507946.669565531177830.0005052774169483260.00444759107869079
POU2F2#545249.106124057742520.000145395665174930.00188656701145539
RFX5#5993412.04791082719514.74457429336527e-050.00082793415977406
RXRA#6256315.055962854350.0004758307997303580.00433982122897903
SIN3A#2594245.408884726815140.001168172384885160.00797716462044075
SP1#666745.69838137814090.0009482606065333980.00685460890682043
SP2#6668426.15353049384462.13562021071447e-067.7606833398333e-05
SPI1#668848.204323508522730.000220661881527680.00249763804539605
STAT3#6774410.51946499715428.16377768286615e-050.00123388824518214
TAF1#687243.343046285745290.008005664898701650.0323081895110129
TBP#690843.706770687096390.005296377814784350.0244875117357237
TCF7L2#6934410.77017656313737.42969445082454e-050.00115675292002037
THAP1#55145431.36914460285131.03171810326891e-064.32390076193025e-05
USF1#739146.361499277207960.0006105011399140830.00508778555310301
ZBTB7A#5134147.35190930787590.000342223540015990.00347173232595726
ZEB1#6935416.88843201754391.22862303393937e-050.0003050063252712



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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