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Coexpression cluster:C1207: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!4.11e-36!102;UBERON:0003061!4.11e-36!102;UBERON:0002193!3.71e-34!112;UBERON:0007023!1.00e-25!115;UBERON:0002371!9.85e-25!80;UBERON:0001474!1.78e-21!86;UBERON:0002405!3.92e-21!115;UBERON:0004765!6.59e-17!101;UBERON:0001434!6.59e-17!101;UBERON:0001049!1.21e-09!57;UBERON:0005068!1.21e-09!57;UBERON:0006241!1.21e-09!57;UBERON:0007135!1.21e-09!57;UBERON:0000178!1.42e-09!15;UBERON:0000179!1.42e-09!15;UBERON:0000463!1.42e-09!15;UBERON:0002780!1.89e-07!41;UBERON:0001890!1.89e-07!41;UBERON:0006240!1.89e-07!41;UBERON:0003080!2.23e-07!42;UBERON:0002616!2.98e-07!59;UBERON:0002384!3.12e-07!375
|ontology_enrichment_uberon=UBERON:0002390!4.11e-36!102;UBERON:0003061!4.11e-36!102;UBERON:0002193!3.71e-34!112;UBERON:0007023!1.00e-25!115;UBERON:0002371!9.85e-25!80;UBERON:0001474!1.78e-21!86;UBERON:0002405!3.92e-21!115;UBERON:0004765!6.59e-17!101;UBERON:0001434!6.59e-17!101;UBERON:0001049!1.21e-09!57;UBERON:0005068!1.21e-09!57;UBERON:0006241!1.21e-09!57;UBERON:0007135!1.21e-09!57;UBERON:0000178!1.42e-09!15;UBERON:0000179!1.42e-09!15;UBERON:0000463!1.42e-09!15;UBERON:0002780!1.89e-07!41;UBERON:0001890!1.89e-07!41;UBERON:0006240!1.89e-07!41;UBERON:0003080!2.23e-07!42;UBERON:0002616!2.98e-07!59;UBERON:0002384!3.12e-07!375
|pathway_enrichment=9.01000184573147e-06;0.00570333116834802;2;50;Type II interferon signaling (IFNG) (Wikipathways):WP619!6.25100917324437e-05;0.0197844440333184;2;131;IL-5 up reg. targets (Netpath):NetPath_17
|pathway_enrichment=9.01000184573147e-06;0.00570333116834802;2;50;Type II interferon signaling (IFNG) (Wikipathways):WP619!6.25100917324437e-05;0.0197844440333184;2;131;IL-5 up reg. targets (Netpath):NetPath_17
|tf_chipseq_enrich=BATF#10538;5:17.3984298516455:2.2818035468994e-06:8.14454137507269e-05!BCL11A#53335;4:16.2111172020612:4.9553880252627e-05:0.00084897600060763!E2F1#1869;5:3.50527801062809:0.00509055358791505:0.0236890044186722!EBF1#1879;4:5.08940962661086:0.00419823316250242:0.0199944946535907!FAM48A#55578;4:660.096428571429:1.88892317757448e-11:2.27540078134604e-09!IRF3#3661;4:26.8468298351369:6.81330236493166e-06:0.000198154966775577!IRF4#3662;4:12.5225786781395:0.000135673113103555:0.00177652510775103!MEF2A#4205;5:13.3880220783172:8.2817757531295e-06:0.000229001953370689!NFKB1#4790;5:3.9200453029956:0.00303658142448461:0.0161188069830621!PAX5#5079;5:4.76397537941274:0.00121882104700747:0.00820024810464555!POU2F2#5452;5:6.50437432695895:0.000276785134033055:0.00294820628386316!REST#5978;4:5.51430212350173:0.00311564137576196:0.0163769927849013!RXRA#6256;4:11.4712097937904:0.000190695857178501:0.00230510238748443!SMC3#9126;4:8.59710448281877:0.000579846628016137:0.00486688113665333!SP1#6667;5:4.07027241295778:0.00254920612899158:0.0141097323072633!SPI1#6688;6:7.03227729301948:2.05436318006376e-05:0.000455145600684511!TCF12#6938;5:7.59604635870459:0.000131112637393808:0.00172437636780908!TCF7L2#6934;5:7.69298325938382:0.000123319885015426:0.00165928954794203!YY1#7528;5:3.50797910703847:0.00507257067280898:0.0236147904295934!ZNF143#7702;4:7.71478660127309:0.000877196960661348:0.00654149042302824
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}}
}}

Revision as of 12:51, 5 September 2012


Full id: C1207_migratory_granulocyte_CD19_CD14_immature_adult_Dendritic



Phase1 CAGE Peaks

Hg19::chr15:45028225..45028238,+p13@TRIM69
Hg19::chr16:10971037..10971076,+p1@CIITA
Hg19::chr16:10971077..10971090,+p2@CIITA
Hg19::chr16:10971094..10971117,+p3@CIITA
Hg19::chr16:10971144..10971153,+p4@CIITA
Hg19::chr16:11004975..11004985,+p@chr16:11004975..11004985
+
Hg19::chr4:185395590..185395627,-p3@IRF2


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


p.valueFDRnGenesnPathwayName
9.01000184573147e-060.00570333116834802250Type II interferon signaling (IFNG) (Wikipathways):WP619
6.25100917324437e-050.01978444403331842131IL-5 up reg. targets (Netpath):NetPath_17



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


GO IDGO nameFDR corrected p-value
GO:0003702RNA polymerase II transcription factor activity0.0164432371661441
GO:0043130ubiquitin binding0.0386029895776261
GO:0032182small conjugating protein binding0.0386029895776261



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
leukocyte9.32e-53140
hematopoietic stem cell4.47e-51172
angioblastic mesenchymal cell4.47e-51172
hematopoietic cell3.00e-49182
hematopoietic oligopotent progenitor cell1.20e-47165
hematopoietic multipotent progenitor cell1.20e-47165
nongranular leukocyte1.15e-46119
hematopoietic lineage restricted progenitor cell1.43e-43124
myeloid cell1.53e-26112
common myeloid progenitor1.53e-26112
macrophage dendritic cell progenitor5.29e-2665
myeloid leukocyte1.37e-2576
granulocyte monocyte progenitor cell4.33e-2571
monopoietic cell1.12e-2463
monocyte1.12e-2463
monoblast1.12e-2463
promonocyte1.12e-2463
CD14-positive, CD16-negative classical monocyte9.09e-2342
myeloid lineage restricted progenitor cell1.76e-2270
classical monocyte5.84e-2045
lymphocyte3.40e-1953
common lymphoid progenitor3.40e-1953
lymphoid lineage restricted progenitor cell1.02e-1852
lymphocyte of B lineage5.79e-1524
pro-B cell5.79e-1524
B cell4.82e-1014
dendritic cell1.67e-0810
connective tissue cell4.17e-08365
mesenchymal cell5.13e-08358
conventional dendritic cell2.09e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.11e-36102
blood island4.11e-36102
hemolymphoid system3.71e-34112
adult organism1.00e-25115
bone marrow9.85e-2580
bone element1.78e-2186
immune system3.92e-21115
skeletal element6.59e-17101
skeletal system6.59e-17101
neural tube1.21e-0957
neural rod1.21e-0957
future spinal cord1.21e-0957
neural keel1.21e-0957
blood1.42e-0915
haemolymphatic fluid1.42e-0915
organism substance1.42e-0915
regional part of forebrain1.89e-0741
forebrain1.89e-0741
future forebrain1.89e-0741
anterior neural tube2.23e-0742
regional part of brain2.98e-0759
connective tissue3.12e-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
BATF#10538517.39842985164552.2818035468994e-068.14454137507269e-05
BCL11A#53335416.21111720206124.9553880252627e-050.00084897600060763
E2F1#186953.505278010628090.005090553587915050.0236890044186722
EBF1#187945.089409626610860.004198233162502420.0199944946535907
FAM48A#555784660.0964285714291.88892317757448e-112.27540078134604e-09
IRF3#3661426.84682983513696.81330236493166e-060.000198154966775577
IRF4#3662412.52257867813950.0001356731131035550.00177652510775103
MEF2A#4205513.38802207831728.2817757531295e-060.000229001953370689
NFKB1#479053.92004530299560.003036581424484610.0161188069830621
PAX5#507954.763975379412740.001218821047007470.00820024810464555
POU2F2#545256.504374326958950.0002767851340330550.00294820628386316
REST#597845.514302123501730.003115641375761960.0163769927849013
RXRA#6256411.47120979379040.0001906958571785010.00230510238748443
SMC3#912648.597104482818770.0005798466280161370.00486688113665333
SP1#666754.070272412957780.002549206128991580.0141097323072633
SPI1#668867.032277293019482.05436318006376e-050.000455145600684511
TCF12#693857.596046358704590.0001311126373938080.00172437636780908
TCF7L2#693457.692983259383820.0001233198850154260.00165928954794203
YY1#752853.507979107038470.005072570672808980.0236147904295934
ZNF143#770247.714786601273090.0008771969606613480.00654149042302824



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.