whole genome annotation of refseq genes on human genome HG19 version: aCGH #genomics
software for genomic annotations on HG19 version of human genome for aCGH experiment with filtration of known CNV polymorphisms in CEU population.
# dependencies: this software is dependent of BEDTOOLS
>sudo apt-get install bedtools
# aCGHarrayDirectHG19 Shell script which allow to remove european CNV polymorphism and to annotate downstream genomic intervals on HG19 human genome especially with cancer genes from COSMIC database, pluripotent genes from Plurinet database, and transcription factor molecules. This script needs the installation of Bedtools utilities in the OS environement. This script also needs dependencies of installing 5 annotation databases in the subfolder DATABASES_HG19: - hg19GENEname_sorted.bed: Refseq HG19 annotations - scandbHG19CEU_sorted.bed: CNV polymorphisms in european population, data derived from http://www.scandb.org/ website - plurinetHG19_sorted.bed: genes that are characterized as belonging to a pluripotency network (PLURINET DB) - CosmicHG19.bed: genes presenting somatic alteration in cancer and leukemia - TFHG19.bed: census database of molecules classed as transcription factor Script needs to be execute in BASH environnement with previous dependencies: USAGE: $sh acgh_direct_HG19.sh example.bed
EXAMPLE FILE: "example.bed" with minimum 5 columns needs to be pass as first parameter of the shell line bed file needs to be place at the parental directory so same the directory than the script! DATABASES : - Transcription factor database (Vaquerizas et al., 2009) - COSMIC database (Futreal et al., 2004) - Plurinet database (Müller et al., 2008) - European CNV polymorphism annotation (Gamazon et al., 2010) - RefSeq annotation database on HG19 (O’Leary et al., 2016) DEPENDENCIES: - Bedtools (Quinlan, 2014) References -Futreal, P.A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., and Stratton, M.R. (2004). A census of human cancer genes. Nat. Rev. Cancer 4, 177–183. -Gamazon, E.R., Zhang, W., Konkashbaev, A., Duan, S., Kistner, E.O., Nicolae, D.L., Dolan, M.E., and Cox, N.J. (2010). SCAN: SNP and copy number annotation. Bioinforma. Oxf. Engl. 26, 259–262. -Müller, F.-J., Laurent, L.C., Kostka, D., Ulitsky, I., Williams, R., Lu, C., Park, I.-H., Rao, M.S., Shamir, R., Schwartz, P.H., et al. (2008). Regulatory networks define phenotypic classes of human stem cell lines. Nature 455, 401–405. -O’Leary, N.A., Wright, M.W., Brister, J.R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016). Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733-745. -Quinlan, A.R. (2014). BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr. Protoc. Bioinforma. 47, 11.12.1-34. -Vaquerizas, J.M., Kummerfeld, S.K., Teichmann, S.A., and Luscombe, N.M. (2009). A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet. 10, 252–263.