Lower right: fragments per kilobase
of transcript per million mapped reads (FPKM) of PSMC3IP.
Abbreviations: Bta-RHO, bovine rhodopsin; EL, extracellular loop; FPKM, fragments per kilobase
of exon per million fragments mapped; GO, gene ontology; GPCR, G-protein-coupled receptor; Gr, gustatory receptor; KEGG, Kyoto Encyclopedia of Genes and Genomes; mRNA, messenger RNA; TM, transmembrane helix; Tpa-OPNGq1, Todarodes pacificus, rhodopsin.
Gene counts were normalized to the values of Reads Per Kilobase
of transcript per Million mapped reads (RPKM).
Following deep sequencing, expression levels of mapped genes were calculated and normalized by reads per kilobase
transcriptome per million mapped reads (RPKM) to eliminate the influence of gene lengths and sequencing discrepancy.
The lncRNA and mRNA sequence reads of the IDD and control groups were normalized to fragments per kilobase
of transcript per million mapped reads (FPKM) values .
Gene expression level analysis was performed by the reads per kilobase
per million mapped reads (RPKM) method using the formula RPKM = 103C/NL, where C is the number of mappable reads that uniquely align to a unigene, N is the total number of mappable reads that uniquely align to all unigenes, and L is the sum of the unigenes in base pairs (Mortazavi et al., 2008).
Expresion diferencial de genes.--El siguiente paso en el analisis de RNA-Seq fue la reconstruccion del transcriptoma y su cuantificacion El nivel de expresion de todos los transcriptos que mapearon en el genoma fue cuantificado como fragmentos por kilobase
de exon por millon de reads (FPKM).
For each of the RefSeq genes, reads uniquely aligned within the genome-mapped exons of that gene were summed and then divided by the sum of the exon lengths to yield reads per kilobase
. The resulting modified raw gene count was then divided by the total number of uniquely aligned reads for the sample, yielding reads per kilobase
per million uniquely mapped reads (RPKM) (15).
All breaks in MLL occur within the same 8 kilobase
(kb) region, (bcr) and create in-frame fusion mRNAs and fusion proteins with the translocation partner gene.
These results provide direct evidence that asbestos fibers induced kilobase
pair deletion mutations in a transgenic mouse mutation system, and that these were mediated by oxyradicals.
These genome-wide technologies use in situ hybridization for SNP detection and contain anywhere from 1,000 to 500,000 SNP markers, with about one marker per five kilobase
, or 5 kb.
A 300 kilobase
interval genetic map of rice including 883 expressed sequences.