Annmap protocols

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Annmap specifications

Information


Unique identifier OMICS_00900
Name Annmap
Interface Web user interface
Restrictions to use None
Biological technology Affymetrix
Computer skills Basic
Stability No
Maintained No

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Publications for Annmap

Annmap in pipelines

 (2)
2014
PMCID: 3899227
PMID: 24466029
DOI: 10.1371/journal.pone.0086329

[…] there was no corresponding plus2 array for the breast cell line mdn., the top four ranking genes from torres-roca et al (rpia, rbbp4, rgs19, znf208) were mapped to affymetrix plus2 probesets using annmap. the corresponding expression data for the probesets were extracted and plotted on a linear scale (anti-log)., gene symbols for the amundson et al gene signature were taken from the second […]

2014
PMCID: 4050258
PMID: 24853205
DOI: 10.1038/ncomms4947

[…] an extensive transcription map of s. pombe. these regions were then positioned relative to known annotation and labelled according to the gene(s) they overlapped, using the bioconductor package annmap. next, we identified for each transcribed locus its 5′- and 3′-extent in a given sample. subsequent analysis was performed in r and bioconductor software unless otherwise stated., […]


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Annmap in publications

 (10)
PMCID: 5372268
PMID: 28359318
DOI: 10.1186/s12967-017-1174-z

[…] 439,778 exonic probe sets (within 38,900 genes) were kept in the analysis, after filtering out intronic, intergenic and unreliable probe sets (according to the nomenclature defined in the r package annmap []). raw data (affymetrix cel files) have been deposited in ncbi’s gene expression omnibus (geo), and are accessible through geo series accession number gse61676. the exon level probe sets […]

PMCID: 5417364
PMID: 28480052
DOI: 10.1038/npjgenmed.2016.20

[…] to edger to call differential expression (absolute fold-change >2 relative to 0 h; false discovery rate (fdr) <1%) at each time point. annotation was supplied by the bioconductor package annmap., functional enrichment analysis was performed using the goseq package in r to identify statistically enriched go terms (hypergeometric test: benjamini and hochberg corrected p value […]

PMCID: 4967825
PMID: 27411892
DOI: 10.1098/rsob.160070

[…] array remained for differential gene expression analysis. annotations and cross-mappings between probesets, exons and genes were obtained from ensembl mouse genome using the r/bioconductor package annmap (bioconductor 2.14)., data were analysed using student's t-test. significant differences are indicates with *p < 0.05 and **p < 0.01., to determine whether sox7-enforced expression […]

PMCID: 4320548
PMID: 25519510
DOI: 10.1186/1471-2164-15-1129

[…] calculated by panp was less than 0.05. for each replicate, the present probesets were mapped to the genes using the ensembl human gene annotation database version 70 via the bioconductor package annmap []. gene lists for one sample were compiled from the two replicates, containing the genes which were present in both replicates., data for the mcf7 and mcf10a samples were generated using […]

PMCID: 4133372
PMID: 25122196
DOI: 10.1371/journal.pone.0105099

[…] and ingenuity systems (redwood city, ca). the rma was used to normalise and summarise the expression values at the probeset level . probesets were mapped to genes using the bioconductor package annmap to position probesets relative to ensembl version 60 annotations . the r package limma was used to find differentially expressed genes and ingenuity to find the enriched pathways […]


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Annmap institution(s)
Cancer Research UK, Bioinformatics Group, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Withington, Manchester, UK

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