Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons

Liu, Yanchen; Tian, Fenfang; Li, Shuiming; Chen, Wei; Gong, Weibo; Xie, Hui; Liu, Dan; Huang, Rongzhong; Liao, Wei; Yi, Faping; Zhou, Jian

doi:10.1007/s00726-021-03058-9

Cited by 4 publications

(4 citation statements)

References 42 publications

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“…Finally, we invoke a supplemental table from an actual study in which the mouse brain proteome was measured after RAB3GAP1 disruption 19 . We plot the supplementary table P -values representing GO-CGL enrichment against our GO-CGL abundance rankings (Table S3).…”

Section: Resultsmentioning

confidence: 99%

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WhatIsMyGene: Back to the Basics of Gene Enrichment

Hodge,

Saethang

2023

Preprint

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WIMG AbstractSince its inception over 20 years ago, gene enrichment has been largely associated with curated gene lists (e.g. GO) that are constructed to represent various biological concepts; the cell cycle, cancer drivers, protein-protein interactions, etc. Researchers expect that a comparison of their own lab-generated lists with curated lists should produce insight. Despite the abundance of such curated lists, we here show that they rarely outperform existing individual lab-generated datasets when measured using standard statistical tests of study/study overlap. This demonstration is enabled by the WhatIsMyGene database, which we believe to be the single largest compendium of transcriptomic and micro-RNA perturbation data. The database also houses voluminous proteomic, cell type clustering, lncRNA, epitranscriptomic (etc.) data. In the case of enrichment tools that do incorporate specific lab studies in underlying databases, WIMG generally outperforms in the simple task of reflecting back to the user known aspects of the input set (cell type, the type of perturbation, species, etc.), enhancing confidence that unknown aspects of the input may also be revealed in the output. A limited number of GO lists are included in the database. However, these lists are assigned backgrounds, meaning that GO lists that are replete with abundant entities do not inordinately percolate to the highest ranking positions in output. We delineate a number of other features that should make WIMG indispensable in answering essential questions such as “What processes are embodied in my gene list?” and “What does my gene do?”

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Section: Resultsmentioning

confidence: 99%

“…CGL enrichment tables may be biased toward abundance. 210 GO-CGLs are assigned P -values in a supplementary table 19 . These values are plotted against abundance rankings for each GO-CGL (R 2 =.23, P = .0008).…”

Section: Resultsmentioning

confidence: 99%

WhatIsMyGene: Back to the Basics of Gene Enrichment

Hodge,

Saethang

2023

Preprint

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“…The RAB3GAP1 and RAB3GAP2 have been linked to the regulation of the RAB GTPase RAB3 and exocytosis of hormones and neurotransmitters at the neuronal synapse. [15][16][17][18] It has been shown in a mouse model of Rab3GAP1/2, significant plays a role in the regulation of Rab18 activity. 5,18 It was reported that RAB3GAP1 and RAB3GAP2 are significant factors involved in autophagy, which is an intracellular, lysosome-dependent degradation process in eukaryotes, and is also involved in vesicular formation, transport, and fusion.…”

Section: Discussionmentioning

confidence: 99%

“…[15][16][17][18] It has been shown in a mouse model of Rab3GAP1/2, significant plays a role in the regulation of Rab18 activity. 5,18 It was reported that RAB3GAP1 and RAB3GAP2 are significant factors involved in autophagy, which is an intracellular, lysosome-dependent degradation process in eukaryotes, and is also involved in vesicular formation, transport, and fusion. In addition, as a vesicular trafficking protein, Rab GTPase regulates various steps of autophagy.…”

Section: Discussionmentioning

confidence: 99%

First Clinical Report of Two RAB3GAP1 Pathogenic Variant in Warburg Micro Syndrome

Akkuş

Duman

2023

J Pediatr Genet

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Warburg micro (WARBM) syndrome is an autosomal recessive disease characterized by severe brain and eye abnormalities. Loss-of-function mutations in RAB18, RAB3GAP2, RAB3GAP1, or TBC1D20 can lead to this disease. Here, we present two unrelated WARBM syndrome patients who had an RAB3GAP1 c.559 C > T, (p.Arg187Ter) and c.520 C > T (p.Arg174Ter) homozygous state. Both patients had microcephaly, microphthalmia, microcornea, bilateral congenital cataracts, severe intellectual disability, and congenital hypotonia. Using the method of next-generation sequencing and sanger sequencing, we found two nonsense variations at the splice site in exon 7 of RAB3GAP1 in the WARBM syndrome patients. The mutations were predicted to cause the syndrome due to the early stop codon, and the patients had the WARBM1 syndrome. We present the first clinical report of two different unreported variants with RAB3GAP1 mutation in the literature.

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