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Data files and other supplementary materials for Lefever et al., 2022 PMID: 35736460

Lefever, Daniel (2022) Data files and other supplementary materials for Lefever et al., 2022 PMID: 35736460. [Dataset]

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Abstract

This data download includes supplementary data for Lefever DE, Miedel MT, Pei F, DiStefano JK, Debiasio R, Shun TY, Saydmohammed M, Chikina M, Vernetti LA, Soto-Gutierrez A, Monga SP, Bataller R, Behari J, Yechoor VK, Bahar I, Gough A, Stern AM, Taylor DL. A Quantitative Systems Pharmacology Platform Reveals NAFLD Pathophysiological States and Targeting Strategies. Metabolites. 2022 Jun 7;12(6):528. doi: 10.3390/metabo12060528. PMID: 35736460; PMCID: PMC9227696.

The following data are included in a zip file: differentially enriched pathways for each pairwise cluster and clinical classification comparison; DEGs resulting for each pairwise cluster and clinical classification comparisons; gene signatures used for CMap analysis; CMAP scores of small molecules with a DrugBank ID for the 24 queries described in the Methods; list of top 20 CMap predictions from both the 2017 and 2020 LINCS databases and both ranking methods (“Best score” and “Percentile score”) from the 24 signatures; degree of the nodes in the NAFLD subnetwork; network proximity-determined Z-scores for the highest ranking CMap-predicted drugs with targets mapping to the NAFLD subnetwork; DEGs resulting from the LAMPS pairwise comparisons (EMS vs. NF, LMS vs. NF, LMS vs. EMS); differentially enriched pathways the LAMPS pairwise comparisons (EMS vs. NF, LMS vs. NF, LMS vs. EMS); the 71 features selected by the final MLENet model; the differentially enriched pathways across 7 NAFLD categories for each pairwise cluster and clinical classification comparison; and NAFLD associated protein interactome.

Data from experimental studies performed in this work are available at: https://mps.csb.pitt.edu/assays/assaystudyset/27/. The R analysis code for this study is available at: https://github.com/lefeverde/QSPpaper.


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Item Type: Dataset
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Lefever, Daniellefeverde@gmail.comdel530000-0003-2274-1881
Date: 7 June 2022
Date Type: Completion
DOI or Unique Handle: 10.3390/metabo12060528
Uncontrolled Keywords: CMap; MAFLD; MPS; NAFLD; NASH; QSP; connectivity map; drug combinations; drug discovery; drug repurposing; fibrosis; liver; lobular inflammation; metabolic-associated fatty liver disease; microphysiology systems; network proximity; non-alcoholic fatty liver disease; non-alcoholic steatohepatitis; quantitative systems pharmacology; steatosis; targeting disease states
Related URLs:
Funders: 1UG3TR003289-01-NIH/NCATS, 4UH3DK119973-03-NIH/NIDDK, 4UH3DK119973-03-NIH/NIDDK, S10OD12269-NIH, U24TR002632-NIH/NCATS, 5U01 TR002383-03-NIH/NCATS, R01 DK097160-NIH/NIDDK, R01 DK088231-NIH/NIDDK, P41 GM103712 NIH/NIGMS, PO1 DK096990 NIH/NIDDK, 1P30DK120531-01
Type of Data: Mixed
Copyright Holders: NA
Date Deposited: 28 Jan 2023 18:57
Last Modified: 02 Feb 2023 18:16
URI: http://d-scholarship.pitt.edu/id/eprint/44129

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