Highly co-expressed gene pairs are shown to be conserved as pairs at about twice the average rate. Physical proximity only accounts for a small proportion of this conservation, demonstrating that purely neutralist models of gene order evolution are not realistic....
Table S1. List of RNA-Seq samples. (DOCX 84 kb) Additional file 2: Table S2. The 303 epithelium scale-to-feather transition (SFT) genes. Column A and B are Ensembl gene ID and gene symbol, respectively. From column C to column F are normalized gene expression levels (CPM) for sample...
Table 2), by examining a larger gene list, we found 787 genes shared by PanA, CA, LA, BIC, and BUC, which are positively co-expressed with DND1 while there are 521 common genes that are conversely co-expressed with DND1 in these five cancer types (q < 0.01; Suppl. Figure 3). 4...
non-conserved and conserved coexpressed gene pairs Chittabrata Mal1, Md Aftabuddin2 and Sudip Kundu1,3* Abstract Background: Analyzing the microarray data of different conditions, one can identify the conserved and condition-specific genes and gene modules, and thus can infer the underlying cellula...
Cell type composition in each spatial transcriptome spots were computed using RCTD v.2.0.130 based on the spot mRNA expression and the marker gene list. For the intestine and SVZ datasets, we directly used cell type annotations from the original study7. Verification in scRNA-seq Dimension ...
Genomic evidence indicates that exoU acquisition is likely mediated by horizontal gene transfer (HGT) of the pathogenicity island PAPI-2, while deletion of exoU was sufficient to mitigate virulence in the exoS+/exoU+ strains. Furthermore, bioinformatics analysis showed that such exoS+/exoU+ P....
a list of lncRNA transcripts and a list of coding transcripts are retrieved as target datasets for each transcriptome. These datasets were screened for relative gene targets of miRNAs, predicted from the assemblies, using psRNAtarget web-tool, with user-defined query and target options at default ...
Despite extensive research, the regulatory mechanisms underlying the pathogenesis and progression of ccRCC remain largely unknown.MethodsWe downloaded 5 ccRCC expression profiles from the Gene Expression Omnibus (GEO) database and obtained the list of differentially expressed genes (DEGs). Using String ...
Besides, the identified DCLs could also be sifted according to their relevance with a selected gene list, for example, DCGs. Table 2 Fractions of DRLs or 'extended DRLs' in DCL sets. Full size table In summary, the results from simulation studies indicate that reasonably designed DCEA ...
Furthermore, GeneAnswers tests each concept for its "enrichment" in the gene list versus the genome using the well-defined hypergeometric statistical test32. These observations gave us a good level of confidence in the obtained results. In order to be more confident about the relationships ...