Functional Interpretation Research Articles

Disregarding multimappers leads to biases in the functional assessment of NGS data

BackgroundStandard ChIP-seq and RNA-seq processing pipelines typically disregard sequencing reads whose origin is ambiguous (“multimappers”). This usual practice has potentially important consequences for the functional interpretation of the data: genomic elements belonging to clusters composed of highly similar members are left unexplored.ResultsIn particular, disregarding multimappers leads to the underrepresentation in epigenetic studies of recently active transposable elements, such as AluYa5, L1HS and SVAs. Furthermore, this common strategy also has implications for transcriptomic analysis: members of repetitive gene families, such the ones including major histocompatibility complex (MHC) class I and II genes, are under-quantified.ConclusionRevealing inherent biases that permeate routine tasks such as functional enrichment analysis, our results underscore the urgency of broadly adopting multimapper-aware bioinformatic pipelines –currently restricted to specific contexts or communities– to ensure the reliability of genomic and transcriptomic studies.

A simple assay for measuring tannin-protein precipitation capacity offers insights into the diet and food choice of black howler monkeys (Alouatta pigra).

Phenolics, like tannins, are plant-specialized metabolites that play a protective role against herbivory. Tannins can reduce palatability and bind with proteins to reduce digestibility, acting as deterrents to feeding and impacting nutrient extraction by herbivores. Some assays measure tannin and total phenolics content in plants but lack determination of their biological effects, hindering the interpretation of tannin function in herbivory and its impacts on animal behavior and ecology. In this study, we successfully applied the radial diffusion assay to assess tannin protein precipitation (PP) capacity and evaluate the anti-nutritional effects of tannins in food plants (n = 24) consumed by free-ranging black howler monkeys (Alouatta pigra) in Tabasco, Mexico. We found PP rings in five plant species consumed by the monkeys. The mature fruit of Inga edulis was the most consumed food plant, despite having a high tannin PP capacity (56.66 mg tannic acid equivalent/g dry matter). These findings highlight the presence of tannins in the black howler diet and provide insight into the primates' resilience and potential strategies for coping with anti-nutritional aspects of the diet.

A Ce2MgMoO6 double perovskite decorated on a functionalized carbon nanofiber nanocomposite for quantification of ciprofloxacin in milk and honey samples: Density functional theory interpretation

In this study, a novel Ce2MgMoO6/CNFs (cerium magnesium molybdite double perovskite decorated on carbon nanofibers) nanocomposite was developed for selective and ultra-sensitive detection of ciprofloxacin (CFX). Physical characterization and analytical techniques were used to explore the morphology, structure, and electrocatalytic characteristics of the Ce2MgMoO6/CNFs nanocomposite. The sensor has a wide linear range (0.005–7.71 μM and 9.75–77.71 μM), a low limit of detection (0.012 μM), high sensitivity (0.807 μA μM−1 cm−2 nM), remarkable repeatability, and an appreciable storage stability. Here, we used density functional theory to investigate CFX and oxidized CFX as well as the locations of the energy levels and electron transfer sites. Furthermore, the Ce2MgMoO6/CNFs-modified electrode was successfully tested in food samples (milk and honey), indicating an acceptable response with a recovery percentage and relative standard deviation of less than 4%, which is comparable to that of GC-MS. Finally, the developed sensor exhibited high selectivity and stability for CFX detection.

MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics.

The wide applications of liquid chromatography - mass spectrometry (LC-MS) in untargeted metabolomics demand an easy-to-use, comprehensive computational workflow to support efficient and reproducible data analysis. However, current tools were primarily developed to perform specific tasks in LC-MS based metabolomics data analysis. Here we introduce MetaboAnalystR 4.0 as a streamlined pipeline covering raw spectra processing, compound identification, statistical analysis, and functional interpretation. The key features of MetaboAnalystR 4.0 includes an auto-optimized feature detection and quantification algorithm for LC-MS1 spectra processing, efficient MS2 spectra deconvolution and compound identification for data-dependent or data-independent acquisition, and more accurate functional interpretation through integrated spectral annotation. Comprehensive validation studies using LC-MS1 and MS2 spectra obtained from standards mixtures, dilution series and clinical metabolomics samples have shown its excellent performance across a wide range of common tasks such as peak picking, spectral deconvolution, and compound identification with good computing efficiency. Together with its existing statistical analysis utilities, MetaboAnalystR 4.0 represents a significant step toward a unified, end-to-end workflow for LC-MS based global metabolomics in the open-source R environment.

Optogenetic inhibition of the orbitofrontal cortex disrupts inhibitory control during stop-change performance in male rats.

Historically, the orbitofrontal cortex (OFC) has been implicated in a variety of behaviors ranging from reversal learning and inhibitory control to more complex representations of reward value and task space. While modern interpretations of the OFC's function have focused on a role in outcome evaluation, these cognitive processes often require an organism to inhibit a maladaptive response or strategy. Single unit recordings from the OFC in rats performing a stop-change task show that the OFC responds strongly to STOP trials. To investigate the role that the OFC plays in stop-change performance we expressed halorhodopsin (eNpHR3.0) in excitatory neurons in the OFC and tested rats on the stop-change task. Previous work suggests that the OFC differentiates between STOP trials based on trial sequence (i.e., gS trials: STOP trials preceded by a GO versus sS trials: STOP trials preceded by a STOP). We found that yellow light activation of the eNpHR3.0 expressing neurons significantly decreased accuracy only on STOP trials that followed GO trials (gS trials). Further, optogenetic inhibition of OFC speeded reaction times on error trials. This suggests that the OFC plays a role in inhibitory control processes, and that this role needs to be accounted for in modern interpretations of OFC function.Significance Statement The orbitofrontal cortex (OFC) is a highly interconnected brain region thought to be essential for healthy cognitive function. Historically, research has implicated the OFC in the inhibition of inappropriate actions, however, more recent work has focused on its role in guiding value-based decision making. Using a modified version of a canonical inhibitory control task in combination with optogenetics, we show that while important for value-based decision making, disruption of excitatory neurons in the OFC impairs inhibitory control processes as well. This highlights the need for theoretical accounts of OFC function to accommodate its role in both types of cognitive processes.

Current advances in circular RNA detection and investigation methods: Are we running in circles?

Circular RNAs (circRNAs), characterized by their closed-loop structure, have emerged as significant transcriptomic regulators, with roles spanning from microRNA sponging to modulation of gene expression and potential peptide coding. The discovery and functional analysis of circRNAs have been propelled by advancements in both experimental and bioinformatics tools, yet the field grapples with challenges related to their detection, isoform diversity, and accurate quantification. This review navigates through the evolution of circRNA research methodologies, from early detection techniques to current state-of-the-art approaches that offer comprehensive insights into circRNA biology. We examine the limitations of existing methods, particularly the difficulty in differentiating circRNA isoforms and distinguishing circRNAs from their linear counterparts. A critical evaluation of various bioinformatics tools and novel experimental strategies is presented, emphasizing the need for integrated approaches to enhance our understanding and interpretation of circRNA functions. Our insights underscore the dynamic and rapidly advancing nature of circRNA research, highlighting the ongoing development of analytical frameworks designed to address the complexity of circRNAs and facilitate the assessment of their clinical utility. As such, this comprehensive overview aims to catalyze further advancements in circRNA study, fostering a deeper understanding of their roles in cellular processes and potential implications in disease. This article is categorized under: RNA Methods > RNA Nanotechnology RNA Methods > RNA Analyses in Cells RNA Methods > RNA Analyses In Vitro and In Silico.

Technological advancements in functional interpretation of genome-wide association studies (GWAS) findings: bridging the gap to clinical translation.

Genome-wide association studies (GWAS) significantly advanced our understanding of the genetic underpinnings of diseases. However, challenges persist, particularly in interpreting non-coding variants in linkage disequilibrium that affect genes in disease-relevant cells. Addressing key obstacles-identifying causal variants, uncovering target genes, and understanding their network impact-is crucial. This graphical review navigates advanced techniques to fully leverage GWAS for future therapeutic breakthroughs.

Fungsi Manajamen dalam Al-Quran dan Hadist: Studi Literatur

Management is an activity that starts from planning, organizing, mobilizing, supervising to coordinate existing resources to achieve common goals in an organization. In the Islamic view, the function of education management reviewed in the Qur'an has several discussions including: (1) planning, (2) organizing; (3) actuating, and (4) controlling. This paper aims to describe verses, hadiths and the relevance between theories and the interpretation of management functions. This research is library research and is included in the qualitative research approach. Data collection is carried out directly from various relevant literature including the Quran, hadith, books, and research articles. Data analysis is carried out qualitatively consisting of data reduction, data presentation, and conclusions. The results of data analysis show that the management function has the word of God that regulates it starting from the functions of planning, organizing, moving and supervising

The Original Technicality of the Human Being

In this article I present the thesis of the original technicality of man proposed by the French philosopher Bernard Stiegler, who passed away in 2020. Stiegler's thought is undergoing continuous re-elaboration due to the singularity of the proposed theses deriving from studies of contemporary anthropology and philosophy. The research method used is subjective-argumentative and interpretive. Reading Stiegler's texts lends itself well to a functional interpretation of the thesis according to which digital technologies are natural prostheses for 21st century students. With the subjective-argumentative methodological approach I can reach a specific goal: demonstrating how the use of digital devices is to be considered an educational asset starting from Stiegler’s philosophy. He makes us understand how the original technicality is decisive for cognitive development. Moreover, the subjective-argumentative approach, as little objective as it may be, offers the flexibility to support a contemporary educational theory such as George Siemens’ Connectivism.

PhuEGO: A Network-Based Method to Reconstruct Active Signaling Pathways From Phosphoproteomics Datasets

Signaling networks are critical for virtually all cell functions. Our current knowledge of cell signaling has been summarized in signaling pathway databases, which, while useful, are highly biased toward well-studied processes, and do not capture context specific network wiring or pathway cross-talk. Mass spectrometry-based phosphoproteomics data can provide a more unbiased view of active cell signaling processes in a given context, however, it suffers from low signal-to-noise ratio and poor reproducibility across experiments. While progress in methods to extract active signaling signatures from such data has been made, there are still limitations with respect to balancing bias and interpretability. Here we present phuEGO, which combines up-to-three-layer network propagation with ego network decomposition to provide small networks comprising active functional signaling modules. PhuEGO boosts the signal-to-noise ratio from global phosphoproteomics datasets, enriches the resulting networks for functional phosphosites and allows the improved comparison and integration across datasets. We applied phuEGO to five phosphoproteomics data sets from cell lines collected upon infection with SARS CoV2. PhuEGO was better able to identify common active functions across datasets and to point to a subnetwork enriched for known COVID-19 targets. Overall, phuEGO provides a flexible tool to the community for the improved functional interpretation of global phosphoproteomics datasets.

Activity reconstitution of Kre33 and Tan1 reveals a molecular ruler mechanism in eukaryotic tRNA acetylation.

RNA acetylation is a universal post-transcriptional modification that occurs in various RNAs. Transfer RNA (tRNA) acetylation is found at position 34 (ac4C34) in bacterial tRNAMet and position 12 (ac4C12) in eukaryotic tRNASer and tRNALeu. The biochemical mechanism, structural basis and functional significance of ac4C34 are well understood; however, despite being discovered in the 1960s and identification of Kre33/NAT10 and Tan1/THUMPD1 as modifying apparatuses, ac4C12 modification activity has never been reconstituted for nearly six decades. Here, we successfully reconstituted the ac4C12 modification activity of yeast Kre33 and Tan1. Biogenesis of ac4C12 is primarily dependent on a minimal set of elements, including a canonical acceptor stem, the presence of the 11CCG13 motif and correct D-arm orientation, indicating a molecular ruler mechanism. A single A13G mutation conferred ac4C12 modification to multiple non-substrate tRNAs. Moreover, we were able to introduce ac4C modifications into small RNAs. ac4C12 modification contributed little to tRNA melting temperature and aminoacylation in vitro and in vivo. Collectively, our results realize in vitro activity reconstitution, delineate tRNA substrate selection mechanism for ac4C12 biogenesis and develop a valuable system for preparing acetylated tRNAs as well as non-tRNA RNA species, which will advance the functional interpretation of the acetylation in RNA structures and functions.

Data collection for assessment of the natural capital at the regional level: case study of LTSER Trnava region

ContextThe landscape provides not only a living space for all life forms, including humans, but also a spatial base and set of resources for the implementation of individual human activities. Inappropriate implementation of human activities, disrespecting the properties of the landscape's natural resources, causes the degradation of natural resources and, consequently, the human living.ObjectivesThe aim of this paper is to develop new methodological procedures and algorithms for effective assessment of natural capital based on the geosystem approach.MethodsEach territorial unit (geosystem) represents a unique combination of natural assets that create a certain potential for the development of individual activities and eco-stabilization functions. In this study, we developed a new approach and algorithms to assess the natural capital of landscapes for sustainable use. This involves selecting indicators and their functional interpretation, as well as collecting available spatial data and statistics for GIS analysis, synthesis, and modeling.ResultsThe methodological procedure consists of the determination of indicators for natural capital assessment, the determination of their functional values and weighting coefficients, the determination of the suitability of the geosystem for the implementation of individual activities based on the value of natural capital, and the determination of restrictions and limiting factors. The set of data on landscape assets can be categorized into abiotic, land cover and biotic, and socio-economic indicators, which can either support human activities or limit them. Options for sustainable use of natural capital were split into two groups of potential activities: (I) natural capital for landscape planning activities and (II) specific activities or functions (e.g., natural capital for energy use, recreation, regulation services). The modeling of eco-stabilizing natural capital in Trnava LTSER pointed to low spatial ecological stability, mainly in the central part of the district.DiscussionDiscussion pointed to strength, novelty and opportunities of implementing methodological approach to natural capital assessment.ConclusionsAs an output of this methodological approach, a comprehensive digital spatial database of landscape-ecological data for the assessment of natural capital and the suitability of its use for socio-economic activities has been created in Slovakia. The database represents a set of consistent spatial information on natural capital assets and other indicators, including land cover and socio-ecological indicators. The methodological approach can be applicable to any territory on the basis of a modification.

Nearest-Neighbour Correlation Functions for the Supersymmetric XYZ Spin Chain and Painlevé VI

We study nearest-neighbour correlation functions for the ground state of the supersymmetric XYZ spin chain with odd length and periodic boundary conditions. Under a technical assumption related to the Q-operator of the corresponding eight-vertex model, we show that they can be expressed exactly in terms of the Painlevé VI tau functions sn\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$s_n$$\\end{document} and s¯n\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{\\bar{s}}}_n$$\\end{document} introduced by Bazhanov and Mangazeev. Furthermore, we give an interpretation of the correlation functions in terms of the Painlevé VI Hamiltonian.

Обвинение как стратегия дискредитации администрации Дж. Байдена в американcкой медиакоммуникации

The phenomenon of verbal aggression in political media journalism attracts the attention of researchers studying various confrontational speech strategies and tactics, including the strategy of discrediting, implemented primarily by the tactics of accusation. The article presents the results of a comprehensive analysis of accusation tactics implementing the speech and behavioral strategy of discrediting the Biden administration on the Tucker Carlson Tonight talk show. Speech strategies, techniques and linguistic means of implementing accusation tactics are revealed. The purpose of the article is to analyze the tactics of accusation that implement the speech and behavioral strategy of discrediting the Biden administration in the Tucker Carlson Tonight show. The source of the research material was the scripts of 31 Tucker Carlson Tonight shows. The empirical basis of the study was 205 contexts discrediting the Biden administration through accusation tactics. The methods of logic and statistics, the system and functional method, description and interpretation were used to analyze the material. The tactics of accusation are more often implemented through a group of explicit speech acts than implicit ones, while each group includes reasoned and undocumented accusations. Common and distinctive speech techniques, morphological, syntactic, lexical and expressive language tools were identified for these groups of speech acts. Statistical data on the analysis of accusation tactics implemented by groups of implicit and explicit speech acts can be presented in the form of a ratio of 1:1.5. Typical means of expression for explicit speech acts are phraseological units and slogans (reasoned and undocumented accusation), for implicit speech acts: hyperbole (reasoned accusation) and the technique of “inappropriate direct speech” (undocumented accusation). The means of expressive syntax are a distinctive feature of implicit and explicit undocumented accusation.

Abstract 6150: MMP14 and MKLN1 as colorectal cancer susceptibility genes and a drug repurposing candidate from genome-wide association study in South Korea

Abstract Background: One of the major topics about colorectal cancer (CRC) is to find susceptible genes. Furthermore, functional interpretation of post-GWAS analysis gains attention and various approaches to find drug-repurposing candidates are used in cancer research. Our study aims to identify susceptible genes for CRC and provide drug-repurposing candidates. Methods: CRC patients in Seoul National University Hospital with prospective follow-up were recruited. From blood-derived DNA, genome-wide SNPs were genotyped using the Korea Biobank Array and 409,063 SNPs were extracted. SNP-based logistic regression model was fit for the event of CRC estimating beta values. Furthermore, post-GWAS analysis was conducted using regulatory function, multiple annotation and gene expression database. Drug-repurposing candidate was identified through the pre-trained deep neural network with susceptible genes. Results: We used 500 participants of CRC cases and 1,500 participants of healthy controls. For GWAS, statistically significant associations were mapped to MKLN1, MMP14, PTPN14 and MKL2 genes. For post-GWAS analysis, strong associations were found for MKLN1 (rs75170436, 7q32.3, Beta=-0.90, P-value=5.90×10-13) and MMP14 (rs3751489, 14q11.2, Beta=-1.91, P-value=2.31×10-12). From the drug-repurposing analysis, PPARδ/β agonist (GW0742; Binding score=3.79(MKLN1), 12.06(MMP14)) was identified for both genes with the highest score. Conclusions: We revealed MKLN1 and MMP14 genes as susceptible genes associated with CRC development. Additionally, we identified PPARδ/β agonist (GW0742) as a drug-repurposing candidate for the treatment of CRC. These findings can promote the understanding of CRC development and provide a novel therapeutic candidate for CRC patients in the future. Citation Format: Dabin Yun, Jung-Ho Yang, Sun-Seong Kweon, Jin-ah Sim, Minjung Kim, Ji Won Park, Seung Yong Jeong, Aesun Shin, Nan Song. MMP14 and MKLN1 as colorectal cancer susceptibility genes and a drug repurposing candidate from genome-wide association study in South Korea [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6150.

Beyond skeletal studies: A computational analysis of nasal airway function in climate adaptation.

Ecogeographic variation in human nasal anatomy has historically been analyzed on skeletal morphology and interpreted in the context of climatic adaptations to respiratory air-conditioning. Only a few studies have analyzed nasal soft tissue morphology, actively involved in air-conditioning physiology. We used in vivo computer tomographic scans of (N = 146) adult individuals from Cambodia, Chile, Russia, and Spain. We conducted (N = 438) airflow simulations during inspiration using computational fluid dynamics to analyze the air-conditioning capacities of the nasal soft tissue in the inflow, functional, and outflow tract, under three different environmental conditions: cold-dry; hot-dry; and hot-humid. We performed statistical comparisons between populations and sexes. Subjects from hot-humid regions showed significantly lower air-conditioning capacities than subjects from colder regions in all the three conditions, specifically within the isthmus region in the inflow tract, and the anterior part of the internal functional tract. Posterior to the functional tract, no differences were detected. No differences between sexes were found in any of the tracts and under any of the conditions. Our statistical analyses support models of climatic adaptations of anterior nasal soft tissue morphology that fit with, and complement, previous research on dry skulls. However, our results challenge a morpho-functional model that attributes air-conditioning capacities exclusively to the functional tract located within the nasal cavity. Instead, our findings support studies that have suggested that both, the external nose and the intra-facial soft tissue airways contribute to efficiently warming and humidifying air during inspiration. This supports functional interpretations in modern midfacial variation and evolution.

Diagnosing schizophrenia using deep learning: Novel interpretation approaches and multi-site validation

Schizophrenia is a profound and enduring mental disorder that imposes significant negative impacts on individuals, their families, and society at large. The development of more accurate and objective diagnostic tools for schizophrenia can be expedited through the employment of deep learning (DL), that excels at deciphering complex hierarchical non-linear patterns. However, the limited interpretability of deep learning has eroded confidence in the model and restricted its clinical utility. At the same time, if the data source is only derived from a single center, the model's generalizability is difficult to test. To enhance the model's reliability and applicability, leave-one-center-out validation with a large and diverse sample from multiple centers is crucial. In this study, we utilized Nine different global centers to train and test the 3D Resnet model's generalizability, resulting in an 82% classification performance (area under the curve) on all datasets sourced from different countries, employing a leave-one-center-out-validation approach. Per our approximation of the feature significance of each region on the atlas, we identified marked differences in the thalamus, pallidum, and inferior frontal gyrus between individuals with schizophrenia and healthy controls, lending credence to prior research findings. At the same time, in order to translate the model's output into clinically applicable insights, the SHapley Additive exPlanations (SHAP) permutation explainer method with an anatomical atlas have been refined, thereby offering precise neuroanatomical and functional interpretations of different brain regions.

Arkady Vasilyevich Sokolov as a documentologist

Our contemporary Arkady Vasilyevich Sokolov (1934–2023) specialized in many disciplines within the documentology sphere, namely library science, bibliography, informatics, noocommunicology, etc., and documentology, in particular. The author focuses on this aspect of Sokolov’s work. His interest in documentology raised naturally from informatics, with his starting point in 1962. Professionally engaged in information search, Sokolov explored the nature of information, which finally culminated in the monograph “The philosophy of information” in 2010. In those days library scientists were willing to become the part of information science persuading – themselves, first of all – that that the library science was an information discipline. Sokolov’s many and rather substantial arguments were contradictory. He criticized reasonably the interpretation of library functions in the 1994 Federal Law “On librarianship” by emphasizing that it was a mistake to set the information function against the others. However, instead of calling for adequate statement functions he tried to rationalize this inaccuracy. Similarly, the inappropriate approach he applied to the comparison of “information” and “document”, “document” and “book’ concepts. Meanwhile, Arkady Sokolov has expanded significantly the field of documentology by introducing the concept of documentosphere into the philosophy of documents. He started developing the concept of Bibliologos that encompasses the whole field of documentology. The author concludes that Arkady V. Sokolov’s contribution to documentology is great and undeniable.

Convolution, deconvolution, the unit hydrograph and flood routing

Convolution equations are used to relate the input and the output of a system such as rainfall and runoff, or inflow and outflow of a river reach. There have been numerous reports of unsatisfactory results from the deconvolution necessary to calculate the connecting transfer function. The cause is that the equations are ill-conditioned, and it is shown here that the fundamental theoretical solution is that of wild oscillations such as has often been found computationally. A spectral method is proposed for numerical solution, where, instead of individual point values, the transfer function is expressed as series of given continuous functions, where the problem is to determine the coefficients of those functions. The resulting equations have been found to be well-conditioned, and solutions obtained were smooth, bounded, and enabled a certain amount of physical interpretation of the transfer function. The method has been applied to several problems, including typical rainfall–runoff ones and flood routing and wave propagation problems, with quite satisfactory results. Another problem for deconvolution is found to be the traditional use of truncated equations. A remedy is only to use later output data points where convolution with input data does not reach back beyond the initial one. For the routing of larger flood events, the linear methods employed were found to be not so accurate. However as they are a first approximation that requires no knowledge of stream geometry or resistance, and as either discharge or water level hydrographs can be used, they may be useful.

MCSdb, a database of proteins residing in membrane contact sites

Organelles do not act as autonomous discrete units but rather as interconnected hubs that engage in extensive communication by forming close contacts called “membrane contact sites (MCSs)”. And many proteins have been identified as residing in MCS and playing important roles in maintaining and fulfilling specific functions within these microdomains. However, a comprehensive compilation of these MCS proteins is still lacking. Therefore, we developed MCSdb, a manually curated resource of MCS proteins and complexes from publications. MCSdb documents 7010 MCS protein entries and 263 complexes, involving 24 organelles and 44 MCSs across 11 species. Additionally, MCSdb orchestrates all data into different categories with multitudinous information for presenting MCS proteins. In summary, MCSdb provides a valuable resource for accelerating MCS functional interpretation and interorganelle communication deciphering.