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abbreviations.tex
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abbreviations.tex
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% General technical terms
\abbrev[principal components analysis]{pca}{\abbrsc{PCA}}
\abbrev[false discovery rate]{fdr}{\abbrsc{FDR}}
\neverexpandabbr{fdr}
\abbrev[read count per kilobase of transcript per million mapped
reads]{rpkm}{\abbrsc{RPKM}}
\abbrev[fragments per kilobase of transcript per million mapped read
pairs]{fpkm}{\abbrsc{FPKM}}
\neverexpandabbr{fpkm}
\abbrev[transcripts per million]{tpm}{\abbrsc{TPM}}
\abbrev[differentially expressed]{de}{\abbrsc{DE}}
% General biological terms
\abbrev[polymerase chain reaction]{pcr}{\abbrsc{PCR}}
\abbrev[high-throughput sequencing]{hts}{\abbrsc{HTS}}
\abbrev[chromatin immunoprecipitation]{chip}{\lowsc{Ch}\abbrsc{IP}}
\abbrev[chromatin immunoprecipitation followed by
sequencing]{chipseq}{\abbr{chip}-seq}
\neverexpandabbr{chipseq}
\abbrev[\abbr{rna} sequencing]{rnaseq}{\abbr{rna}-seq}
\neverexpandabbr{rnaseq}
\abbrev[\abbr{trna} adaptation index]{tai}{\lowsc{t}\abbrsc{AI}}
\newcommand*\nucleotide[1]{\seq{#1}\xspace}
\newcommand*\nA{\nucleotide A}
\newcommand*\nC{\nucleotide C}
\newcommand*\nG{\nucleotide G}
\newcommand*\nT{\nucleotide T}
\newcommand*\nU{\nucleotide U}
\newcommand*\nI{\nucleotide I}
\abbrev[codon usage]{cu}{\abbrsc{CU}}
\abbrev[relative codon usage]{rcu}{\abbrsc{RCU}}
\abbrev[relative anticodon abundance]{raa}{\abbrsc{RAA}}
\abbrev[codon usage bias]{cub}{\abbrsc{CUB}}
\abbrev[anticodon abundance bias]{aab}{\abbrsc{AAB}}
\abbrev{gc}{\abbrsc{GC}}
% Gene-related
\abbrev[deoxyribonucleic acid]{dna}{\abbrsc{DNA}}
\abbrev[complementary \abbr{dna}]{cdna}{\lowsc{c}\abbr{dna}}
\abbrev[ribonucleic acid]{rna}{\abbrsc{RNA}}
\abbrev[messenger \abbr{rna}]{mrna}{\lowsc{m}\abbr{rna}}
\abbrev[transfer \abbr{rna}]{trna}{\lowsc{t}\abbr{rna}}
\abbrev[ribosomal \abbr{rna}]{rrna}{\lowsc{r}\abbr{rna}}
\abbrev[non-coding \abbr{rna}]{ncrna}{\lowsc{nc}\abbr{rna}}
\abbrev[long non-coding \abbr{rna}]{lncrna}{\lowsc{lnc}\abbr{rna}}
\abbrev[\abbr{rna}-induced silencing complex]{risc}{\abbrsc{RISC}}
\newcommand*\xtrna[2][]{\ensuremath{\text{\abbr{trna}}_\text{#1}^\text{#2}}}
\abbrev[short interspersed nuclear element]{transsine}{\abbrsc{SINE}}
\abbrev[long interspersed nuclear element]{transline}{\abbrsc{LINE}}
\abbrev[transcription start site]{tss}{\abbrsc{TSS}}
\abbrev[transcription factor]{tf}{\abbrsc{TF}}
\abbrev[untranslated region]{utr}{\abbrsc{UTR}}
\abbrev[\seq{CCCTC}-binding factor]{ctcf}{\abbrsc{CTCF}}
\abbrev[transcription factor \abbrsc{III} B]{tfiiib}{\abbrsc{TFIIIB}}
\neverexpandabbr{tfiiib}
\abbrev[transcription factor \abbrsc{III} C]{tfiiic}{\abbrsc{TFIIIC}}
\neverexpandabbr{tfiiic}
\abbrev[\seq{TATA} binding protein]{tbp}{\abbrsc{TBP}}
\newcommand*\pol[1]{\csuse{pol#1}}
\abbrev{pol1}{pol~\abbrsc{I}}
\abbrev{pol2}{pol~\abbrsc{II}}
\abbrev{pol3}{pol~\abbrsc{III}}
\abbrev[\abbr{dna}-dependent \abbr{rna} polymerase \abbrsc{I}]{Pol1}{Pol~\abbrsc{I}}
\abbrev[\abbr{dna}-dependent \abbr{rna} polymerase \abbrsc{II}]{Pol2}{Pol~\abbrsc{II}}
\abbrev[\abbr{dna}-dependent \abbr{rna} polymerase \abbrsc{III}]{Pol3}{Pol~\abbrsc{III}}
\newcommand*\fivep{\num{5}\ensuremath{'}\xspace}
\newcommand*\threep{\num{3}\ensuremath{'}\xspace}
% Databases
\abbrev[\abbrsc{NCBI} mouse genome build 37]{ncbim37}{\abbrsc{NCBIM37}}
\abbrev[Genome Reference Consortium Mouse Build 38]{grcm38}{\abbrsc{GRC}\lowsc{m}38}
\abbrev[Gene Expression Omnibus]{geo}{\abbrsc{GEO}}
\abbrev[Gene Ontology]{go}{\abbrsc{GO}}
% Species
\newcommand*\mmu{\species{mmu}}
\newcommand*\hsa{\species{hsa}}
\abbrev[type-1 human immunodeficiency virus]{hivi}{\abbrsc{HIV}-1}
% Other
\newcommand*\etc{\mbox{\&\kern-0.2ex \itshape\scalefont{0.9}c}}