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Coexpression cluster:C3394: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189557003733319!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324253944180366!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321170027037718!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460908037927042!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155756413611978!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108491134795504!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246729398576291!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.032479540923563!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470161469991909!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172577869050448!SREBF2#6721;1:145.647754137116:0.00685021551456999:0.0290447246722221!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541556282756503!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390011571413608!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328508087507215
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189557003733319!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324253944180366!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321170027037718!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460908037927042!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155756413611978!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108491134795504!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246729398576291!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.032479540923563!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470161469991909!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172577869050448!SREBF2#6721;1:145.647754137116:0.00685021551456999:0.0290447246722221!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541556282756503!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390011571413608!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328508087507215
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,2.47502,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,3.32688,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,1.55552,1.48681,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,6.63372,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,2.56478
}}
}}

Revision as of 16:06, 26 November 2012


Full id: C3394_Eosinophils_CD14_cerebellum_pineal_Neutrophils_CD4_Peripheral



Phase1 CAGE Peaks

Hg19::chr14:102414651..102414721,+p@chr14:102414651..102414721
+
Hg19::chr2:157198916..157198978,-p2@NR4A2
Hg19::chr5:98264867..98264903,+p1@ENST00000513175


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


GO IDGO nameFDR corrected p-value
GO:0042053regulation of dopamine metabolic process0.00500412104085718
GO:0042069regulation of catecholamine metabolic process0.00500412104085718
GO:0042417dopamine metabolic process0.00917422190823815
GO:0006584catecholamine metabolic process0.0133443227756191
GO:0018958phenol metabolic process0.0133443227756191
GO:0042133neurotransmitter metabolic process0.0133443227756191
GO:0006576biogenic amine metabolic process0.0243950900741787
GO:0001505regulation of neurotransmitter levels0.0243950900741787
GO:0006575amino acid derivative metabolic process0.0250206052042859
GO:0003707steroid hormone receptor activity0.0292741080890145
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0316169465763249
GO:0004879ligand-dependent nuclear receptor activity0.0319012716354645
GO:0006725aromatic compound metabolic process0.0352213134798794
GO:0030182neuron differentiation0.0362798775462145
GO:0045893positive regulation of transcription, DNA-dependent0.0362798775462145
GO:0048699generation of neurons0.0362798775462145
GO:0022008neurogenesis0.0362798775462145
GO:0045941positive regulation of transcription0.0362798775462145
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0362798775462145
GO:0007268synaptic transmission0.0362798775462145
GO:0019226transmission of nerve impulse0.0393180938924492
GO:0031325positive regulation of cellular metabolic process0.0415114586343834
GO:0009893positive regulation of metabolic process0.042535028847286
GO:0006357regulation of transcription from RNA polymerase II promoter0.0440988166725538
GO:0006066alcohol metabolic process0.0445366772636289



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
leukocyte9.99e-28136
classical monocyte1.51e-2442
CD14-positive, CD16-negative classical monocyte1.51e-2442
myeloid leukocyte2.23e-2472
defensive cell9.21e-2448
phagocyte9.21e-2448
hematopoietic lineage restricted progenitor cell3.98e-23120
nongranular leukocyte1.07e-21115
myeloid lineage restricted progenitor cell5.16e-2066
granulocyte monocyte progenitor cell3.90e-1967
hematopoietic stem cell5.82e-19168
angioblastic mesenchymal cell5.82e-19168
hematopoietic cell1.44e-18177
macrophage dendritic cell progenitor1.90e-1861
monopoietic cell4.27e-1859
monocyte4.27e-1859
monoblast4.27e-1859
promonocyte4.27e-1859
hematopoietic oligopotent progenitor cell4.53e-17161
hematopoietic multipotent progenitor cell4.53e-17161
myeloid cell8.16e-13108
common myeloid progenitor8.16e-13108
stuff accumulating cell1.37e-0987
Uber Anatomy
Ontology termp-valuen
adult organism3.82e-26114
hematopoietic system9.12e-2198
blood island9.12e-2198
neural tube3.89e-1956
neural rod3.89e-1956
future spinal cord3.89e-1956
neural keel3.89e-1956
bone marrow5.35e-1976
regional part of nervous system7.98e-1853
regional part of brain7.98e-1853
hemolymphoid system1.10e-17108
bone element1.60e-1782
skeletal element5.09e-1590
regional part of forebrain6.99e-1541
forebrain6.99e-1541
anterior neural tube6.99e-1541
future forebrain6.99e-1541
immune system2.13e-1493
skeletal system2.44e-13100
brain5.58e-1268
future brain5.58e-1268
brain grey matter8.92e-1234
gray matter8.92e-1234
telencephalon1.57e-1134
neural plate2.02e-1182
presumptive neural plate2.02e-1182
regional part of telencephalon5.73e-1132
cerebral hemisphere9.69e-1132
neurectoderm1.97e-1086
central nervous system2.47e-1081
regional part of cerebral cortex1.39e-0822
nervous system1.96e-0889
cerebral cortex3.58e-0825
pallium3.58e-0825
neocortex7.74e-0820
pre-chordal neural plate1.46e-0761


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#90536.336201576962630.003930750035764890.0189557003733319
E2F1#186934.907389214879320.008460985347239390.0324253944180366
E2F6#187635.017155731697390.00791769806886330.0321170027037718
ELF1#199734.258097958807540.01295179875054610.0460908037927042
GTF2B#2959221.29588662288280.002878180589911410.0155756413611978
HMGN3#932438.178547723350590.001827766942164210.0108491134795504
HNF4A#3172215.42152690863580.005444210486686610.0246729398576291
MEF2A#4205212.4954872730960.008235029478029740.032479540923563
NRF1#4899312.21027944771090.0005492172401020010.00470161469991909
PAX5#507936.669565531177830.003370290999677260.0172577869050448
SREBF2#67211145.6477541371160.006850215514569990.0290447246722221
TAF7#6879311.43306940492390.0006690181981945830.00541556282756503
TFAP2A#7020211.01242291536330.01054990655215560.0390011571413608
YY1#752834.911170749853860.008441455341808260.0328508087507215



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.