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A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with <t>C2_carnitine.</t> C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).
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oral gavage  (MedChemExpress)
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A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with <t>C2_carnitine.</t> C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).
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l carnitine  (Fisher Scientific)
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A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with <t>C2_carnitine.</t> C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).
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d4 l carnitine avanti polar lipids inc  (Croda International Plc)
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A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with <t>C2_carnitine.</t> C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).
D4 L Carnitine Avanti Polar Lipids Inc, supplied by Croda International Plc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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l carnitine lc  (Shanghai Macklin Biochemical)
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A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with <t>C2_carnitine.</t> C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).
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l carnitine  (Beiersdorf Inc)
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A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with <t>C2_carnitine.</t> C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).
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A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with <t>C2_carnitine.</t> C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).
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l carnitine  (Thermo Fisher)
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A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with <t>C2_carnitine.</t> C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).
L Carnitine, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cardiolipin mix  (Croda International Plc)
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Croda International Plc cardiolipin mix
A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with <t>C2_carnitine.</t> C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).
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A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with C2_carnitine. C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).

Journal: bioRxiv

Article Title: Lemonite: identification of regulatory metabolites through data-driven, interpretable integration of transcriptomics and metabolomics data

doi: 10.64898/2026.03.27.714373

Figure Lengend Snippet: A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with C2_carnitine. C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).

Article Snippet: Cells were treated with C2_carnitine (Larodan, 17-0200-7), trigonelline (Sigma-Aldrich, 1686411) or α-glycerophosphocholine (Santa Cruz, sc-301813) at concentrations ranging between 100μM and 10 nM (100 μM, 10 μM, 1 μM, 100 nM, 10 nM and 0).

Techniques: Biomarker Discovery, Gene Expression, Concentration Assay