Dataset Information

Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins.

ABSTRACT: Using data from 183 public human data sets from PRIDE, a machine learning model was trained to identify tissue and cell-type specific protein patterns. PRIDE projects were searched with ionbot and tissue/cell type annotation was manually added. Data from physiological samples were used to train a Random Forest model on protein abundances to classify samples into tissues and cell types. Subsequently, a one-vs-all classification and feature importance were used to analyze the most discriminating protein abundances per class. Based on protein abundance alone, the model was able to predict tissues with 98% accuracy, and cell types with 99% accuracy. The F-scores describe a clear view on tissue-specific proteins and tissue-specific protein expression patterns. In-depth feature analysis shows slight confusion between physiologically similar tissues, demonstrating the capacity of the algorithm to detect biologically relevant patterns. These results can in turn inform downstream uses, from identification of the tissue of origin of proteins in complex samples such as liquid biopsies, to studying the proteome of tissue-like samples such as organoids and cell lines.

SUBMITTER: Claeys T

PROVIDER: S-EPMC10088018 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins.

Claeys Tine T Menu Maxime M Bouwmeester Robbin R Gevaert Kris K Martens Lennart L

Journal of proteome research 20230324 4

Using data from 183 public human data sets from PRIDE, a machine learning model was trained to identify tissue and cell-type specific protein patterns. PRIDE projects were searched with ionbot and tissue/cell type annotation was manually added. Data from physiological samples were used to train a Random Forest model on protein abundances to classify samples into tissues and cell types. Subsequently, a one-vs-all classification and feature importance were used to analyze the most discriminating p ...[more]

PMID: 36963412

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Project description:BackgroundTheoretical models have emphasized systems-level abnormalities in major depressive disorder (MDD). For unbiased yet rigorous evaluations of pathophysiological mechanisms underlying MDD, it is critically important to develop data-driven approaches that harness whole-brain data to classify MDD and evaluate possible normalizing effects of targeted interventions. Here, using an experimental therapeutics approach coupled with machine learning, we investigated the effect of a pharmacological challenge aiming to enhance dopaminergic signaling on whole-brain response to reward-related stimuli in MDD.MethodsUsing a double-blind, placebo-controlled design, we analyzed functional magnetic resonance imaging data from 31 unmedicated MDD participants receiving a single dose of 50 mg amisulpride (MDDAmisulpride), 26 MDD participants receiving placebo (MDDPlacebo), and 28 healthy control subjects receiving placebo (HCPlacebo) recruited through two independent studies. An importance-guided machine learning technique for model selection was used on whole-brain functional magnetic resonance imaging data probing reward anticipation and consumption to identify features linked to MDD (MDDPlacebo vs. HCPlacebo) and dopaminergic enhancement (MDDAmisulpride vs. MDDPlacebo).ResultsHighly predictive classification models emerged that distinguished MDDPlacebo from HCPlacebo (area under the curve = 0.87) and MDDPlacebo from MDDAmisulpride (area under the curve = 0.89). Although reward-related striatal activation and connectivity were among the most predictive features, the best truncated models based on whole-brain features were significantly better relative to models trained using striatal features only.ConclusionsResults indicate that in MDD, enhanced dopaminergic signaling restores abnormal activation and connectivity in a widespread network of regions. These findings provide new insights into the pathophysiology of MDD and pharmacological mechanism of antidepressants at the system level in addressing reward processing deficits among depressed individuals.

Project description:MotivationMetagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Because of the large volume of metagenomics datasets, binning methods need fast and accurate algorithms that can operate with reasonable computing requirements. While standard alignment-based methods provide state-of-the-art performance, compositional approaches that assign a taxonomic class to a DNA read based on the k-mers it contains have the potential to provide faster solutions.ResultsWe propose a new rank-flexible machine learning-based compositional approach for taxonomic assignment of metagenomics reads and show that it benefits from increasing the number of fragments sampled from reference genome to tune its parameters, up to a coverage of about 10, and from increasing the k-mer size to about 12. Tuning the method involves training machine learning models on about 10(8) samples in 10(7) dimensions, which is out of reach of standard softwares but can be done efficiently with modern implementations for large-scale machine learning. The resulting method is competitive in terms of accuracy with well-established alignment and composition-based tools for problems involving a small to moderate number of candidate species and for reasonable amounts of sequencing errors. We show, however, that machine learning-based compositional approaches are still limited in their ability to deal with problems involving a greater number of species and more sensitive to sequencing errors. We finally show that the new method outperforms the state-of-the-art in its ability to classify reads from species of lineage absent from the reference database and confirm that compositional approaches achieve faster prediction times, with a gain of 2-17 times with respect to the BWA-MEM short read mapper, depending on the number of candidate species and the level of sequencing noise.Availability and implementationData and codes are available at http://cbio.ensmp.fr/largescalemetagenomicsContactpierre.mahe@biomerieux.comSupplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins.

Publications

Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins.

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