Jie, W. | Search bioRxiv

bioRxiv2024

DMRIntTk: integrating different DMR sets based on density peak clustering

BackgroundIdentifying differentially methylated regions (DMRs) is a basic task in DNA methylation analysis. However, due to the different strategies adopted, different DMR sets will be predicted on the same dataset, which poses a challenge in selecting a reliable and comprehensive DMR set for downstream analysis. ResultsHere, we develop DMRIntTk, a toolkit for integrating DMR sets predicted by different methods on a same dataset. In DMRIntTk, the genome is segmented into bins and the reliability of each DMR set at different methylation thresholds is evaluated. Then, the bins are weighted based on the covered DMR sets and integrated into DMRs by using a density peak clustering algorithm. To demonstrate the practicality of DMRIntTk, DMRIntTk was applied to different scenarios, including different tissues with relatively large methylation differences, cancer tissues versus normal tissues with medium methylation differences, and disease tissues versus normal tissues with subtle methylation differences. The results show that DMRIntTk can effectively trim the regions with small methylation differences in the original DMR sets and therefore it can enhance the proportion of DMRs with higher methylation differences. In addition, the overlap analysis suggests that the integrated DMR sets are quite comprehensive, and the functional analysis indicates the integrated disease-related DMR sets are significantly enriched in biological pathways, which are associated with the pathological mechanisms of the diseases. ConclusionsConclusively, DMRIntTk can help researchers obtaining a reliable and comprehensive DMR set from many prediction methods.

bioinformatics↗

bioRxiv2021

FishExp: a comprehensive database and analysis platform for gene expression and alternative splicing of fish species

The publicly archived RNA-seq data has grown exponentially, but its valuable information has not yet been fully discovered and utilized, especially for alternative splicing. This is true for fish species, which play important roles in ecology, research, and the food industry. To mitigate this, we present FishExp, a web-based data platform covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes. In addition to searching by gene identifiers and symbols, FishExp allows users to query the data using various functional terms and BLAST alignment. Notably, the user can customize experiments and tools to perform differential/specific expression and alternative splicing analysis, provided with functional enrichments. The results of retrieval and analysis can be visualized on the gene-, transcript- and splicing event-level webpage in a highly interactive and intuitive manner. The manually curated sample information, uniform data processing and visualization tools make it efficient for users to gain new insights from these large datasets. All data in FishExp can be downloaded for more in-depth analysis. FishExp is freely accessible at https://bioinfo.njau.edu.cn/fishExp.

bioinformatics↗

bioRxiv2018

Upregulation of photosynthetic capacity and thylakoid membrane protein enhanced tolerance to heat stress in wucai (Brassica campestris L.)

The hot climate of southern China from late summer to early fall is one of the major factors limiting the yield and quality of wucai (Brassica campestris L.). Under high temperature stress, heat-tolerant cultivars presented moderate injury to the photosynthesic apparatus, less inhibition of photochemical activity, better osmotic adjustment and antioxidant defences capacity compared to heat-sensitive cultivars. To study the effects of high temperature on the growth and development of wucai, plants of WS-1 (heat-tolerant) and WS-6 (heat-sensitive) were exposed to four heat stress treatments in growth chambers for 3 days. Chloroplasts of two cultivars evaluated for photosynthetic characteristics, fatty acid composition and differentially expressed proteins of thylakoid membrane. The chlorophyll (Chl) content was markedly reduced by heat stress, inhibiting photochemical activity. However, larger decreases in growth and photosynthetic parameters [net photosynthetic rate (PN), stomatal conductance (GS), intercellular CO2 concentration (Ci), and leaf transpiration rate (E)] occurred under heat stress in WS-6, compared with WS-1. In addition, WS-6 showed an obviouse K point in O-J-I-P steps under extremely high temperature, which indicated OEC had been damaged. WS-1 showed higher of maximum quantum yield of primary PSII photochemistry (FV/FM), number of active reaction centres per cross section of PSII (RC/CSM), average absorbed photon flux per cross section of PSII (ABS/CSM), maximum trapped exciton flux per cross section of PSII (TR0/CSM), electron transport flux from QA to QB per cross section of PSII (ET0/ CSM) and performance index on absorption basis (PIABS) which indicated greater heat stability in terms of PSII function under higher temperature. Compared to WS-6, WS-1 showed higher membrane stability and photochemical efficiency, and greater increase of saturated fatty acids (SFA), especially palmitic acid under heat stress. WS-1 had higher recovery rate compared to WS-6 after 41{degrees}C heat stress treatment. Additionally, two-dimensional blue native/SDS-PAGE analysis of chloroplast was carried out to compare the differentially expressed proteins between two cultivars. We obtained seven major protein complexes included supercomplexes, PSI-LHCII/PSII monomer, PSII monomer, CP43 less PSII/ATP synthase, LHCII trimer, LHCII monomer and ATP synthase after first dimentional seperation in both cultivars after the first dimensional separation. Then ten differential membrane proteins included light-harvesting Chl a/b-binding (LHC) protein, ATP synthase subunit alpha, ATP synthase subunit beta, photosystem I P700 chlorophyll a apoprotein A2, photosystem II CP43 reaction center protein, photosystem II D2 protein and photosystem II\n\nOS have been found between WS-1 and WS-6. These differentially proteins in cellular membranes could contribute to the differential level of heat tolerance between two wucai cultivars. Our results demonstrated that the heat-tolerant cultivar WS-1 had a greater capacity for photosynthesis and membrane stability by upregulating proteins abundance including light harvesting (light-harvesting Chl a/b-binding protein), energy metabolism (ATPase), and proteins of PSII reaction center (D2, CP43) under heat stress.

biochemistry↗