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Coexpression cluster:C1644: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249452126405676!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352256562139458!E2F6#1876;4:4.01372458535791:0.00663211823393388:0.0282888215737725!EGR1#1958;4:3.99054327584811:0.006780098300144:0.0287579371469252!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447257520705199!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.0011692564200216!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386539216539634!SMARCB1#6598;3:10.9516294686944:0.00151187284834318:0.00965031710109483!SMC3#9126;3:9.0269597069597:0.00265096444946755:0.0146341813065142!ZEB1#6935;3:10.1330592105263:0.00189555692435707:0.0111595304184289
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249452126405676!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352256562139458!E2F6#1876;4:4.01372458535791:0.00663211823393388:0.0282888215737725!EGR1#1958;4:3.99054327584811:0.006780098300144:0.0287579371469252!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447257520705199!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.0011692564200216!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386539216539634!SMARCB1#6598;3:10.9516294686944:0.00151187284834318:0.00965031710109483!SMC3#9126;3:9.0269597069597:0.00265096444946755:0.0146341813065142!ZEB1#6935;3:10.1330592105263:0.00189555692435707:0.0111595304184289
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}}
}}

Revision as of 15:01, 26 November 2012


Full id: C1644_Neutrophils_Eosinophils_medial_amygdala_frontal_paracentral_insula



Phase1 CAGE Peaks

Hg19::chr11:77122928..77123045,-p1@PAK1
Hg19::chr12:90103081..90103155,-p2@ATP2B1
Hg19::chr14:71788096..71788143,+p3@SIPA1L1
Hg19::chr7:26331560..26331647,+p1@SNX10
Hg19::chr7:26331652..26331663,+p7@SNX10


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
leukocyte1.59e-37136
nongranular leukocyte5.66e-32115
hematopoietic lineage restricted progenitor cell1.53e-31120
hematopoietic oligopotent progenitor cell5.94e-31161
hematopoietic multipotent progenitor cell5.94e-31161
hematopoietic stem cell1.17e-30168
angioblastic mesenchymal cell1.17e-30168
myeloid leukocyte1.55e-2972
hematopoietic cell8.53e-26177
granulocyte monocyte progenitor cell1.03e-2567
macrophage dendritic cell progenitor5.88e-2561
classical monocyte1.04e-2442
CD14-positive, CD16-negative classical monocyte1.04e-2442
monopoietic cell3.31e-2459
monocyte3.31e-2459
monoblast3.31e-2459
promonocyte3.31e-2459
defensive cell3.36e-2448
phagocyte3.36e-2448
myeloid lineage restricted progenitor cell6.30e-2466
myeloid cell2.45e-22108
common myeloid progenitor2.45e-22108
lymphocyte3.41e-0853
common lymphoid progenitor3.41e-0853
lymphoid lineage restricted progenitor cell3.96e-0852
nucleate cell6.32e-0855
lymphocyte of B lineage4.09e-0724
pro-B cell4.09e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.21e-2798
blood island6.21e-2798
bone marrow3.74e-2376
bone element3.95e-2282
hemolymphoid system7.01e-21108
skeletal element2.09e-1990
immune system3.31e-1793
skeletal system4.12e-17100
neural tube3.72e-1656
neural rod3.72e-1656
future spinal cord3.72e-1656
neural keel3.72e-1656
regional part of nervous system3.03e-1553
regional part of brain3.03e-1553
regional part of forebrain3.81e-1541
forebrain3.81e-1541
anterior neural tube3.81e-1541
future forebrain3.81e-1541
central nervous system7.55e-1481
telencephalon2.12e-1334
brain grey matter3.47e-1334
gray matter3.47e-1334
cerebral hemisphere3.78e-1332
regional part of telencephalon1.41e-1232
nervous system3.41e-1289
brain4.56e-1268
future brain4.56e-1268
regional part of cerebral cortex1.55e-1122
adult organism1.04e-10114
neocortex1.54e-1020
cerebral cortex2.85e-0925
pallium2.85e-0925
musculoskeletal system1.47e-08167


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
CTCF#1066455.360256373075030.0002259278299937090.00249452126405676
E2F1#186954.907389214879320.0003512818099256460.00352256562139458
E2F6#187644.013724585357910.006632118233933880.0282888215737725
EGR1#195843.990543275848110.0067800983001440.0287579371469252
ELF1#199743.406478367046030.01235066105299550.0447257520705199
PAX5#507956.669565531177837.57493746384605e-050.0011692564200216
RAD21#588548.284027116365060.0004011622639122450.00386539216539634
SMARCB1#6598310.95162946869440.001511872848343180.00965031710109483
SMC3#912639.02695970695970.002650964449467550.0146341813065142
ZEB1#6935310.13305921052630.001895556924357070.0111595304184289



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.