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Bekkar2018 - MAPK1-3 regulation in atherosclerosis

ABSTRACT: This network was obtained by combining (with an OR logical operator) the following list of MAPK1_3 activators: PDGFRB - reference in pubmed:19742316 PDGFB AND (NOT glyoxal) - reference in pubmed:17504976 PARP1 - reference in pubmed:23770291 LEP - reference in pubmed:9815153 PDGFB AND (NOT methylglyoxal) - reference in pubmed:17504976 oxLDL - reference in pubmed:19176597 IL1B_secretion - reference in pubmed:19727662

SUBMITTER: Bekkar A

PROVIDER: MODEL1712240003 | BioModels | 2018-11-16

REPOSITORIES: BioModels

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Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation.

Bekkar Amel A Estreicher Anne A Niknejad Anne A Casals-Casas Cristina C Bridge Alan A Xenarios Ioannis I Dorier Julien J Crespo Isaac I

Database : the journal of biological databases and curation 20180101

<h4>Database url</h4>http://biomodels.caltech.edu. ...[more]

PMID: 29688381

Publication: 1/7

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Bekkar2018 - PPARA regulation in atherosclerosis

Project description:This network was obtained by combining (with an OR logical operator) the following list of PPARA activators: SIRT1 AND PPARGC1A - reference in pubmed:23770291 (NOT MAPK14) AND PPARGC1A - reference in pubmed:24744784 SIRT1 - reference in pubmed:23770291 PPARGC1A - reference in pubmed:23223635 TNF AND PPARGC1A - reference in pubmed:23223635

2018-11-16 | MODEL1712240001 | BioModels

Bekkar2018 - IL1B secretion and regulation in atherosclerosis

Project description:This network was obtained by combining (with an OR logical operator) the following list of IL1B_secretion activators: TXNIP AND IL1B - reference in pubmed:23747245 IL1B AND hydrogen_peroxide - reference in pubmed:20023662 NLRP3_PYCARD_CASP1_complex AND IL1B AND cholesterol_crystal - reference in pubmed:23747245 IL1B AND NLRP3 AND hydrogen_peroxide - reference in pubmed:20023662 IL1B AND oxLDL AND TLR4 - reference in pubmed:23812099 IL1B AND glucose - reference in pubmed:20023662 IL1B AND IL1B_secretion - reference in pubmed:23747245 IL1B AND CASP8 - reference in pubmed:22365665 NLRP3_PYCARD_CASP1_complex AND NFE2L2 AND IL1B - reference in pubmed:23747245 PYCARD AND IL1B AND hydrogen_peroxide - reference in pubmed:20023662 IL1B AND NLRP3 AND glucose - reference in pubmed:20023662 NFE2L2 AND IL1B - reference in pubmed:23747245 IL1B AND mitochondrial_respiratory_chain_complex_I - reference in pubmed:21124315 TXNIP AND IL1B AND glucose - reference in pubmed:20023662 IL1B AND oxLDL AND CD36 - reference in pubmed:23812099 IL1B AND ripoptosome - reference in pubmed:22365665 NLRP3_PYCARD_CASP1_complex AND IL1B - reference in pubmed:23747245

2018-11-16 | MODEL1712240002 | BioModels

Effects of daf-2 mutation, dietary restriction and age on C.elegans proteome

Project description:The overarching project goal was to describe proteome differences between long- and normal-living C.elegans worms. The associated publications are http://www.ncbi.nlm.nih.gov/pubmed/24555535 http://www.ncbi.nlm.nih.gov/pubmed/24002365

2015-05-13 | PXD002161 | Pride

Comparing the transcriptome of naïve C57BL/6 CD44+/+ vs CD44-/- alveolar macrophages

Project description:Purpose: Determine if alveolar macrophage express different transcriptional programs when CD44 expression is lost. Methods: Alveolar macrophages were isolated from the bronchoalveolar lavage of 6-10 week old CD44+/+ and CD44-/- female mice. RNA was isolated an sequenced using Illumina NextSeq 500. RNA was sequenced by the UBC Biomedical Research Center. RNA quality, 18S and 28S ribosomal RNA with RIN = 9.6, was determined by Agilent 2100 Bioanalyzer following standard protocol for NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with paired end 42bp 42bp reads. De-multiplexed read sequences were then aligned to the Mus musculus (mm10) reference sequence using Spliced Transcripts Alignment to a Reference, STAR (https://www.ncbi.nlm.nih.gov/pubmed/23104886), aligners. Results and conclusion: Multiple pathways were abnormal in CD44-/- alveolar macrophages, in particular those involved in lipid metabolism and immune signaling.

2020-01-17 | GSE138445 | GEO

Communication of prostate cancer cells with bone cells via extracellular vesicle RNA; a potential mechanism of metastasis

Project description:Analysis of miRNA and mRNA within extracellular vesicles obtained from prostate cancer PC3 cells. Kaighn ME, et al. Establishment and characterization of a human prostatic carcinoma cell line (PC-3). Invest. Urol. 17: 16-23, 1979. PubMed: 447482

2018-09-01 | GSE117744 | GEO

Gastric Cancer Study GC_126

Project description:126 gastric tissues (90 tumor, 14 lymphnode and 22 normal) assayed using 44K human arrays against common reference (CRG). Published by Leung et al, PNAS, 2002 (PubMed ID 12456890) and Chen et al, MBC, 2003. A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Series_overall_design: Using regression correlation Keywords: other

2005-05-25 | GSE2701 | GEO

Arthritis and Rheumatism

Project description:Synovial tissue mRNA from 21 RA patients and 9 OA patients is hybridized against a common reference sample on lymphochips. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-12-17 | GSE3848 | GEO

Normal placenta

Project description:Total RNA was isolated from all the placental tissues using Trizol, and mRNA was isolated using FastTrack Kit. We used a placenta reference as a standard for all these array hybridizations. The placenta reference is a mixture of placenta mRNA with CRG. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2006-03-09 | GSE4421 | GEO

Normal_human_tissues

Project description:Array hybridizations profiling diverse human tissues; for each array the human tissue RNA is hybridized against a universal reference RNA. Series_type: Logical set Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: other

2005-02-21 | GSE2193 | GEO