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By using Gene (http://www.ncbi.nlm.nih.gov/gene/) of the NCBI, the location of the PPAR gene was determined on the chromosome corresponding species.
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We hence tested if the type 2 diabetes CpG-SNPs that exhibit differential DNA methylation and are located in gene introns or exons are associated with differentially expressed exons assessed by splice index using Gene Array Analyzer (http://GAA.mpi-bn.mpg.de) [ 17].
A subset of VvTPS encoding sesquiterpene synthases were codon-optimized for expression in E. coli, using gene synthesis by DNA2.0 https://www.dna20.com/ and subcloned into the pET-3a or pET-Duet1 expression plasmids (Novagen, http://www.emdchemicals.com).
Selected genes were represented by heat map using GENE-E software (http://www.broadinstitute.org/cancer/software/GENE-E).
Complementary DNA (cDNA) sequences (i.e., without introns) for lncRNAs were obtained querying the Ensembl (http://www.ensembl.org/) data portal through its R/Bioconductor (http://www.bioconductor.org) interface provided by package biomaRt and by using Entrez gene identifiers (http://www.ncbi.nlm.nih.gov/gene).nih.gov/gene
The glucocorticoid responsive element (GRE), androgen responsive element (ARE) and C/EBPβ binding sites were predicted on pig 3β-HSD gene promoter, by using TF Search (http://www.cbrc.jp/research/db/TFSEARCH.html) and gene-regulation (http://www.gene-regulation.com/pub/programs.html) online resources.
Thus, in the present study we analyzed the chromosomal localization of renal sexually dimorphic genes by using GeneTrail Software (http://genetrail.bioinf.uni-sb.de [27]).
Putative genes were annotated by using BlastX (http://www.ncbi.nlm.nih.gov/blast) and the predicted transcripts were also compared with A. gambiae transcripts in Vectorbase (www.vectorbase.org).org
Sequence homology of TaSUT2A, TaSUT2B and TaSUT2D with other cereal SUT genes was analyzed by using DNAMAN (http://www.lynnon.com/pc/alignm.html), and their respective coding sequences were identified by using Open Reading Frame (ORF) finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html).html
We then identified similar gene sequences in GenBank by using blastn (http://www.ncbi.nlm.nih.gov/blast).nih.gov/blast
To identify the functions of miR-183 in HCC cells, we analyzed putative target genes by using the TargetScan http://www.targetscan.org bioinformatics tools [ 18]. miR-183 maybe play the role of oncogene, considering it is up-regulated in HCC.
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