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GNPS - Molecular networking as a dereplication strategy -Figure 4

ABSTRACT: Molecular networking as a dereplication strategy. Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Wong WR, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC. J Nat Prod. 2013 Sep 27;76(9):1686-99. doi: 10.1021/np400413s PubMedID: 24025162 RAW Files used to generate Figure 4. Bacterial network with a cosine similarity score cutoff of 0.65. This network was generated from direct infusion of extracts or direct nanoDESI-MS/MS sampling of eight bacteria, 14 known compounds

INSTRUMENT(S): LTQ FT

ORGANISM(S): Data From Multiple Bacteria

SUBMITTER: Dorrestein and Gerwick

PROVIDER: MSV000078547 | GNPS | Tue Feb 11 14:08:00 GMT 2014

REPOSITORIES: GNPS

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Molecular networking as a dereplication strategy.

Yang Jane Y JY Sanchez Laura M LM Rath Christopher M CM Liu Xueting X Boudreau Paul D PD Bruns Nicole N Glukhov Evgenia E Wodtke Anne A de Felicio Rafael R Fenner Amanda A Wong Weng Ruh WR Linington Roger G RG Zhang Lixin L Debonsi Hosana M HM Gerwick William H WH Dorrestein Pieter C PC

Journal of natural products 20130911 9

A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized or ...[more]

PMID: 24025162

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GNPS - Molecular networking as a dereplication strategy-Figure 3

Project description:Molecular networking as a dereplication strategy. Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Wong WR, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC. J Nat Prod. 2013 Sep 27;76(9):1686-99. doi: 10.1021/np400413s PubMedID: 24025162 RAW Files used to generate Figure 3. Cyanobacterial network with a cosine similarity score cutoff of 0.65. This network was generated when extracts of cyanobacteria (six distinct collections) were separated into nine fractions based on polarity and then analyzed via LC-MS/MS with five known compounds

2014-02-11 | MSV000078548 | GNPS

Smooth muscle cell mineralocorticoid receptor regulation of vascular microRNAs with aging

Project description:We used a smooth muscle cell-specific mineralocorticoid receptor knockout mouse to generate young and aged MR-intact and SMC-MR-KO aortic miRNA to examine the effect of age on vascular miRNA alterations in the presence and absence of SMC-MR. For more information about the mouse model see: McCurley, A et al. Direct regulation of blood pressure by smooth muscle cell mineralocorticoid receptors. Nat Med. 2012 Sep;18(9):1429-33

2016-07-29 | GSE84960 | GEO

Smooth muscle cell mineralocorticoid receptor regulation of vascular mRNAs with aging

Project description:We used a smooth muscle cell-specific mineralocorticoid receptor knockout mouse to generate young and aged MR-intact and SMC-MR-KO aortic mRNA to examine the effect of age on vascular mRNA alterations in the presence and absence of SMC-MR. For more information about the mouse model see: McCurley, A et al. Direct regulation of blood pressure by smooth muscle cell mineralocorticoid receptors. Nat Med. 2012 Sep;18(9):1429-33

2017-08-10 | GSE102397 | GEO

Molecular networking as a dereplication strategy.

Project description: Not available

| S-EPMC3936340 | biostudies-literature

Smooth muscle cell mineralocorticoid receptor regulation of vascular microRNAs with aging

2016-07-29 | E-GEOD-84960 | biostudies-arrayexpress

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.

Project description: Not available

| S-EPMC6786971 | biostudies-literature

Discovery of the p53 targetome in MCF7 cells from RNA-seq and ChIP-seq data

Project description:This SuperSeries is composed of the SubSeries listed below. iRegulon: from a gene list to a gene regulatory network using large motif and track collections. RekinM-bM-^@M-^Ys Janky, Annelien Verfaillie, Hana ImrichovM-CM-!, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval Sanchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean-Christophe Marine, and Stein Aerts. PLOS Computational Biology, 2014. Refer to individual Series

2014-05-27 | E-GEOD-47043 | biostudies-arrayexpress

GNPS - Viequeamides Cyclic Depsipeptides from a Rivularia sp.

Project description:Paper title: Viequeamide A, a Cytotoxic Member of the Kulolide Superfamily of Cyclic Depsipeptides from a Marine Button Cyanobacterium Author List: Boudreau PD, Byrum T, Liu WT, Dorrestein PC, Gerwick WH. Citation: J Nat Prod. 2012 Sep 28;75(9):1560-70. DOI: 10.1021/np300321b PubMedID: 22924493 Brief Description of Data Submitted: MS2 spectra of M+H of Viequeamides B-F collected on an LTQ-FT in either FT or LTQ mode. These spectra were used to determine the structures of Viequeamides C-F with comparison to the Viequeamide B NMR structure. Also uploaded are the MS2 spectra of M+Na of Viequeamide A and B from a low-resolution Thermo LCQ spectrometer (not used in this publication).

2014-04-16 | MSV000078594 | GNPS

Perilous Sites: High basic Fibroblast Growth Factor level supplement Parkinson’s disease pathology and its Spread

Project description:Lewy body (LB) pathology and loss of dopaminergic neurons are imprints of Parkinson’s disease (PD). LBs are mainly comprised of alpha-Synuclein (Dijkstra et al., 2014). Strolling detection of LBs in brain regions contribute to progressive construct of PD pathology to which molecular mechanisms are not clear (H. Braak & Del Tredici, 2017). Two key facets of LB formation are protein aggregation via misfolding and transmission of misfoldled proteins to various brain regions, eventually causing neuronal death (Goedert, Spillantini, Del Tredici, & Braak, 2013; Pacelli et al., 2015). Misfolding requires alterations in intracellular physiology (Carbone, Costa, Provensi, Mannaioni, & Masi, 2017; Funes et al., 2014; Guzman et al., 2018; Pacelli et al., 2015) and detection of misfolded proteins in exosomes confirms exosomatic transmission (Ngolab et al., 2017). High levels of neurotropic-factors (Brockmann et al., 2017) and changes in bioenergetics are found in PD patients, these can bring physiological alterations (Smith et al., 2018). En masse, these evidences and hipocampal association with synucleopathies (Flores-Cuadrado, Ubeda-Bañon, Saiz-Sanchez, de la Rosa-Prieto, & Martinez-Marcos, 2016) allowed us to probe other volunerable PD proteins in cell-lysate and exosomal proteomes of bFGF treated hippocampal neurons. Using WPCNA we developed co-expression modules and spotted many PD related proteins; which can act as precursors during diseased or onset stage.

2020-07-21 | PXD015969 | Pride

The Global Landscape of Multiscale Transcriptomic Networks and Key Regulators in Parkinson’s Disease

Project description:Despite the advance of genetic and genomic analysis of Parkinson’s disease (PD), our understanding of PD pathophysiology remains limited due to unclear etiology of idiopathic PD and unavailable integrated approach for large-scale multi-dimensional data. Herein we report a novel multiscale network approach to establish transcriptomic network from postmortem PD brain data. The analysis delineates structures of gene-gene regulatory networks in PD and identifies novel network regulators that are functionally connected to previously identified PD risk genes. We identify STMN2, encoding a neuron-specific stathmin family protein and down-regulated in PD brains, as the top regulator of the transcriptomic network underlying PD. Knock-down of Stmn2 in mice validates its regulatory role, and Stmn2 deficient mice show dopaminergic neuron vulnerability, phosphorylated a-synuclein elevation, and locomotor function deficits. As predicted from the network analysis, reduced STMN2 expression impairs synaptic vesicle trafficking in midbrain neurons. Our approach sheds light on the complexity of PD pathogenic network and thus facilitates identification of novel PD therapeutic targets.

2019-12-03 | GSE114840 | GEO

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