Genevestigator V3: A Reference Expression Database for   the Meta‐Analysis of Transcriptomes

Hrúz, Tomás; Laule, Oliver; Szabó, Gábor; Wessendorp, Frans; Bleuler, Stefan; Oertle, Lukas; Widmayer, Peter; Gruissem, Wilhelm; Zimmermann, Philip

doi:10.1155/2008/420747

Cited by 1,722 publications

(1,717 citation statements)

References 9 publications

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“…P ‐values indicate statistical significance in expression between low‐ and high‐risk groups. (B, C) Expression of PAK1 and PAK2 in haematological diseases according to the Genevestigator database (Hruz et al , 2008). Asterisks mark samples of BCR / ABL 1 + chronic myeloid leukaemia.…”

Section: Resultsmentioning

confidence: 99%

“…As expression data in chronic myeloid leukaemia (CML) or acute lymphoblastic leukaemia (ALL) are not covered by the SurvExpress database, we switched to a different platform (Genevestigator; https://genevestigator.com/gv/; Hruz et al , 2008) which provides data of BCR/ABL1 ‐driven diseases. This platform allows the ranking of haematopoietic diseases based on the expression level of a given gene.…”

Section: Resultsmentioning

confidence: 99%

“…Patients suffering from different haematological disease entities were divided into low‐ and high‐risk groups according to Aguirre‐Gamboa et al (2013), and levels of PAK1 and PAK2 expression were assessed. Expression of PAK1‐6 was assessed with the publicly available software Genevestigator (https://genevestigator.com/gv/; Hruz et al , 2008). Only disease categories with ≥20 samples were included, and the top 20 hits were shown.…”

Section: Methodsmentioning

confidence: 99%

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Expansion of BCR/ABL1⁺ cells requires PAK2 but not PAK1

et al. 2017

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SummaryThe p21‐activated kinases (PAKs) are key nodes in oncogenic signalling pathways controlling growth, survival, and motility of cancer cells. Their activity is increased in many human cancers and is associated with poor prognosis. To date, PAK deregulation has mainly been studied in solid tumours, where PAK1 and PAK4 are the main isoforms deregulated. We show that PAK1 and PAK2 are the critical isoforms in a BCR/ABL1 + haematopoietic malignancy. In suspension, leukaemic cells deficient for PAK1 and PAK2 undergo apoptosis, while the loss of either protein is well tolerated. Transfer of medium conditioned by shPAK2‐ but not shPAK1‐expressing leukaemic cells interferes with endothelial cell growth. We found that leukaemic cells produce exosomes containing PAK2. Transfer of isolated exosomes supports endothelial cell proliferation. In parallel, we found that leukaemic cells explicitly require PAK2 to grow towards an extracellular matrix. PAK2‐deficient cells fail to form colonies in methylcellulose and to induce lymphomas in vivo. PAK2 might therefore be the critical isoform in leukaemic cells by controlling tumour growth in a dual manner: vascularization via exosome‐mediated transfer to endothelial cells and remodelling of the extracellular matrix. This finding suggests that the PAK2 isoform represents a promising target for the treatment of haematological diseases.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Expansion of BCR/ABL1⁺ cells requires PAK2 but not PAK1

et al. 2017

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“…NIP7;1 is most highly expressed in developing anthers where it is proposed to deliver boron to developing pollen [16] but is also present in many other tissues in both roots and shoots ( Fig. 1) [17].…”

Section: Highlightsmentioning

confidence: 99%

“…NIP7;1 is expressed in several different tissues throughout the inflorescence, shoot and root. Data were obtained from the GENEVESTIGATOR database [17]. Values are means AE SEs plotted on a log 2 scale.…”

Section: Arsenic Content Analysesmentioning

confidence: 99%

Arabidopsis thaliana NIP7;1 is involved in tissue arsenic distribution and tolerance in response to arsenate

Lindsay

Maathuis

2016

FEBS Letters

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The Arabidopsis aquaglyceroporin NIP7;1 is involved in uptake and tolerance to the trivalent arsenic species arsenite. Here, we show that NIP7;1 is also involved in the response to pentavalent arsenate. Loss of function of NIP7;1 improved tolerance to arsenate and reduced arsenic levels in both the phloem and xylem, resulting in altered arsenic distribution between tissues. There was no clear correlation between growth and shoot arsenic concentration. This is the first report detailing the involvement of a NIP transporter in response to arsenate. The data suggest that these proteins are relevant targets for breeding and engineering arsenic tolerance in crops.

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Structure prediction analysis of human core TIM23 complex reveals conservation of the protein translocation mechanism

Maruszczak,

Draczkowski,

Wnorowski

et al. 2024

FEBS Open Bio

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The majority of mitochondrial proteins are encoded in the nucleus, translated on cytosolic ribosomes, and subsequently targeted to the mitochondrial surface. Their further import into the organelle is facilitated by highly specialized protein translocases. Mitochondrial precursor proteins that are destined to the mitochondrial matrix and, to some extent, the inner membrane, utilize translocase of the inner membrane (TIM23). This indispensable import machinery has been extensively studied in yeast. The translocating unit of the TIM23 complex in yeast consists of two membrane proteins, Tim17 and Tim23. In contrast to previous findings, recent reports demonstrate the primary role of Tim17, rather than Tim23, in the translocation of newly synthesized proteins. Very little is known about human TIM23 translocase. Human cells have two orthologs of yeast Tim17, TIMM17A and TIMM17B. Here, using computational tools, we present the architecture of human core TIM23 variants with either TIMM17A or TIMM17B, forming two populations of highly similar complexes. The structures reveal high conservation of the core TIM23 complex between human and yeast. Interestingly, both TIMM17A and TIMM17B variants interact with TIMM23 and reactive oxygen species modulator 1 (ROMO1); a homolog of yeast Mgr2, a protein that can create a channel‐like structure with Tim17. The high structural conservation of proteins that form the core TIM23 complex in yeast and humans raises an interesting question about mechanistic and functional differences that justify existence of the two variants of TIM23 in higher eukaryotes.

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Genevestigator V3: A Reference Expression Database for the Meta‐Analysis of Transcriptomes

Cited by 1,722 publications

References 9 publications

Expansion of BCR/ABL1⁺ cells requires PAK2 but not PAK1

Expansion of BCR/ABL1⁺ cells requires PAK2 but not PAK1

Arabidopsis thaliana NIP7;1 is involved in tissue arsenic distribution and tolerance in response to arsenate

Structure prediction analysis of human core TIM23 complex reveals conservation of the protein translocation mechanism

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Genevestigator V3: A Reference Expression Database for the Meta‐Analysis of Transcriptomes

Cited by 1,722 publications

References 9 publications

Expansion of BCR/ABL1+ cells requires PAK2 but not PAK1

Expansion of BCR/ABL1+ cells requires PAK2 but not PAK1

Arabidopsis thaliana NIP7;1 is involved in tissue arsenic distribution and tolerance in response to arsenate

Structure prediction analysis of human core TIM23 complex reveals conservation of the protein translocation mechanism

Contact Info

Product

Resources

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Expansion of BCR/ABL1⁺ cells requires PAK2 but not PAK1

Expansion of BCR/ABL1⁺ cells requires PAK2 but not PAK1