Mr.Vc v2: An updated version of database with increased data of transcriptome and experimental validated interactions

Abstract

Mr.Vc is a database of curated Vibrio cholerae transcriptome data and annotated information. The main objective is to facilitate the accessibility and reusability of the rapidly growing Vibrio cholerae omics data and relevant annotation. To achieve these goals, we performed manual curation on the transcriptome data and organized the datasets in an experiment-centric manner. We collected unknown operons annotated through text-mining analysis that would provide more clues about how Vibrio cholerae modulates gene regulation. Meanwhile, to understand the relationship between genes or experiments, we performed gene co-expression analysis and experiment-experiment correlation analysis. In additional, functional module named “Interactions” which dedicates to collecting experimentally validated interactions about Vibrio cholerae from public databases, MEDLINE documents and literature in life science journals. To date, Mr.Vc v2, which is significantly increased from the previous version, contains 107 microarray experiments, 106 RNA-seq experiments, and 3 Tn-seq projects, covering 56,839 entries of DEGs (Differentially Expressed Genes) from transcriptomes and 7,463 related genes from Tn-seq, respectively. and a total of 270,129 gene co-expression entries and 11,990 entries of experiment-experiment correlation was obtained, in total 1,316 entries of interactions were collected, including 496 protein-chemical signaling molecule interactions, 472 protein–protein interactions, 306 TF (Transcription Factor)-gene interactions and 42 Vibrio cholerae-virus interactions, most of which obtained from 402 literature through text-mining analysis. To make the information easier to access, Mr.Vc v2 is equipped with a search widget, enabling users to query what they are interested in. Mr.Vc v2 is freely available at http://mrvcv2.biownmc.info.

BBSdb, an open resource for bacterial biofilm-associated proteins

“…anaerobic planktonic cultures, and Experiment_3: biofilm vs. planktonic cultures), in which the expression abundances were normalized as TPM values 11 , using a cutoff of |log2 FC| > 1.5 (FC, fold change) and p-value <0.05 to define DEGs between experiments 12 . We found that the number of DEGs in Experiments1, 2, and 3 were 614, 1507, and 2252, respectively.…”

“…We calculated DEGs of 3 RNA-seq experiments for E. coli ( Experiment_1 : aerobic biofilm cultures vs. aerobic planktonic cultures, Experiment_2 : anaerobic biofilm cultures vs. anaerobic planktonic cultures, and Experiment_3 : biofilm vs. planktonic cultures), in which the expression abundances were normalized as TPM values 11 , using a cutoff of |log2 FC|□ > □ 1.5 (FC, fold change) and p-value <0.05 to define DEGs between experiments 12 . We found that the number of DEGs in Experiments1, 2, and 3 were 614, 1507, and 2252, respectively.…”

“…We analyzed cleaned transcriptome and proteome data using differential expressed analysis, and obtaining 57,385 DEGs and 13,605 DEPs, in which we used a cutoff of |log2 FC| > 1.5 (FC, fold change) and p-value <0.05 to define differentially expressed genes and proteins between experiments (Zhang et al, 2019). In addition, we calculated ‘Top 5% differentially expressed gene’ of 16 different bacteria species, which was proposed by our previous research (Zhang et al, 2022).…”

“…In addition, we calculated 'Top 5% differentially expressed gene' of 16 different bacteria species, which was proposed by our previous research (Zhang et al, 2022).…”

An in-depth analysis and exploreation with focus on the biofilm inStaphylococcus aureus

“…The utilization of a differential fold ranking method, while rudimentary, overlooks certain genes with pivotal roles yet minute variations in expression, thus diverting from the research focus (40). GSEA emerges as a methodology concentrating on whether a preordained gene assembly exhibits systemic differential expression, proffering a panoramic view of biological processes, pathways, or functionalities (41).…”