Integrative omics analysis
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cancer (GC) lacks serum biomarkers with clinical diagnostic value. Multi-omics analysis is an important approach to discovering cancer biomarkers. This study aimed to identify and validate serum biomarkers for GC diagnosis by cross-analysis of proteomics and transcriptomics datasets.
13p vishanshan 27-06-2024 2 1 Download
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Our study aims to explore the relationship, shared gene signature, and the underlying mechanisms that connect rheumatoid arthritis (RA) to colorectal cancer (CRC). RA might be associated with a slight increased risk of CRC. MYO9A is a shared gene signature and a potential immune-related therapeutic target for both CRC and RA.
16p vikoch 27-06-2024 1 1 Download
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Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients’ treatment options.
22p vibransone 28-03-2024 3 2 Download
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Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy.
24p vibransone 28-03-2024 2 1 Download
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Non-coding regulatory elements (NCREs), such as enhancers, play a crucial role in gene regulation, and genetic aberrations in NCREs can lead to human disease, including brain disorders. The human brain is a complex organ that is susceptible to numerous disorders.
27p vibransone 28-03-2024 7 2 Download
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Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches.
17p vicwell 29-02-2024 5 2 Download
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Part 2 book "Comprehensive analysis of parasite biology" includes content: Methods to investigate metabolic systems in trypanosoma; the role of metabolomics in antiparasitic drug discovery; the importance of targeting lipid metabolism in parasites for drug discovery; carbon metabolism of plasmodium falciparum; mathematical modeling and omic data integration to understand dynamic adaptation of apicomplexan parasites and identify pharmaceutical targets; ... and other contents.
255p muasambanhan03 02-01-2024 7 2 Download
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Juvenile Pilocytic Astrocytomas (JPAs) are one of the most common pediatric brain tumors, and they are driven by aberrant activation of the mitogen-activated protein kinase (MAPK) signaling pathway. RAF-fusions are the most common genetic alterations identified in JPAs, with the prototypical KIAA1549-BRAF fusion leading to loss of BRAF’s auto-inhibitory domain and subsequent constitutive kinase activation.
13p vileonardodavinci 23-12-2023 4 3 Download
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EphrinA (EFNA) are Eph receptor ligands that regulate various disease processes. Nonetheless, the expression characteristics of EFNAs in pan-cancer, their relationship with tumor immune microenvironment, and prognostic value landscape remain unknown.
18p vialfrednobel 23-12-2023 6 4 Download
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It is common that cancer patients have different molecular signatures even though they have similar clinical features, such as histology, due to the heterogeneity of tumors. To overcome this variability, we previously developed a new approach incorporating prior biological knowledge that identifies knowledge-driven genomic interactions associated with outcomes of interest.
11p visteverogers 24-06-2023 5 3 Download
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Rapidly evolving high-throughput technology has made it cost-effective to collect multilevel omic data in clinical and biological studies. Different types of omic data collected from these studies provide both shared and complementary information, and can be integrated into association analysis to enhance the power of identifying novel disease-associated biomarkers.
4p vihagrid 30-01-2023 5 3 Download
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The advance of high-throughput technologies has made it cost-effective to collect diverse types of omic data in large-scale clinical and biological studies. While the collection of the vast amounts of multi-level omic data from these studies provides a great opportunity for genetic research, the high dimensionality of omic data and complex relationships among multi-level omic data bring tremendous analytic challenges.
12p vihagrid 30-01-2023 10 3 Download
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In studies with multi-omics data available, there is an opportunity to investigate interdependent mechanisms of biological causality. The GAW20 data set includes both DNA genotype and methylation measures before and after fenofibrate treatment. Using change in triglyceride (TG) levels pre- to posttreatment as outcome, we present a mediation analysis that incorporates methylation.
5p vihagrid 30-01-2023 7 3 Download
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Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data.
21p vialfrednobel 29-01-2022 9 0 Download
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A growing number of single-cell sequencing platforms enable joint profiling of multiple omics from the same cells. We present Cobolt, a novel method that not only allows for analyzing the data from joint-modality platforms, but provides a coherent framework for the integration of multiple datasets measured on different modalities.
21p viarchimedes 26-01-2022 16 0 Download
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To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies.
24p viarchimedes 26-01-2022 11 0 Download
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Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to systematically integrate transcriptomic, epigenomic, and cistromic information to accurately define the regulatory networks critical for metastasis.
28p viarchimedes 26-01-2022 11 0 Download
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Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational strategies to analyze data from complex experimental designs that include multiple data modalities and multiple groups of samples.
17p viarchimedes 26-01-2022 7 0 Download
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Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome.
13p vibeauty 23-10-2021 12 1 Download
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In the present report, a multi-omics integrative analysis, including of the proteomic, transcriptomic and miRNAs, combined with morphological and physiological analysis were conducted.
18p vitzuyu2711 29-09-2021 19 1 Download