GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists

Carmona-Sáez, Pedro; Chagoyen, Mónica; Tirado, Francisco; Carazo, José Marı́a; Pascual-Montano, Alberto

doi:10.1186/gb-2007-8-1-r3

Cited by 559 publications

(325 citation statements)

References 26 publications

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“…Identified differential proteins were manually assigned to mouse official gene IDs, according to the protein names, for further gene list analysis using GeneCodis3 (http://genecodis.cnb.csic.es/) (Carmona‐Saez et al, 2007; Nogales‐Cadenas et al, 2009; Tabas‐Madrid et al, 2012). …”

Section: Methodsmentioning

confidence: 99%

Proteomic differences in recombinant CHO cells producing two similar antibody fragments

Sommeregger

Mayrhofer

Steinfellner

et al. 2016

Biotech & Bioengineering

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Chinese hamster ovary (CHO) cells are the most commonly used mammalian hosts for the production of biopharmaceuticals. To overcome unfavorable features of CHO cells, a lot of effort is put into cell engineering to improve phenotype. “Omics” studies investigating elevated growth rate and specific productivities as well as extracellular stimulus have already revealed many interesting engineering targets. However, it remains largely unknown how physicochemical properties of the recombinant product itself influence the host cell. In this study, we used quantitative label‐free LC‐MS proteomic analyses to investigate product‐specific proteome differences in CHO cells producing two similar antibody fragments. We established recombinant CHO cells producing the two antibodies, 3D6 and 2F5, both as single‐chain Fv‐Fc homodimeric antibody fragments (scFv‐Fc). We applied three different vector strategies for transgene delivery (i.e., plasmid, bacterial artificial chromosome, recombinase‐mediated cassette exchange), selected two best performing clones from transgene variants and transgene delivery methods and investigated three consecutively passaged cell samples by label‐free proteomic analysis. LC‐MS‐MS profiles were compared in several sample combinations to gain insights into different aspects of proteomic changes caused by overexpression of two different heterologous proteins. This study suggests that not only the levels of specific product secretion but the product itself has a large impact on the proteome of the cell. Biotechnol. Bioeng. 2016;113: 1902–1912. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

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Section: Methodsmentioning

confidence: 99%

Proteomic differences in recombinant CHO cells producing two similar antibody fragments

Sommeregger

Mayrhofer

Steinfellner

et al. 2016

Biotech & Bioengineering

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“…GO analysis was performed using the GeneCoDis2.0 web server (Carmona-Saez et al 2007;Nogales-Cadenas et al 2009). The D. melanogaster organism is supported on this server, and GO categories ''Biological Process,'' ''Molecular Function,'' and ''Cellular Component'' were selected.…”

Section: Go Analysismentioning

confidence: 99%

The Drosophila melanogaster transcriptome by paired-end RNA sequencing

Daines

Wang

Wang³

et al. 2010

Genome Res.

130

104

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RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64-100-bp paired-end reads were generated on the Illumina GA II yielding 3563 sequencing coverage. More than 95% of FlyBase genes and 90% of splicing junctions were observed. Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel splicing events. A total of 319 novel transcripts were identified, representing a 2% increase over the current annotation. Alternate splicing was observed in 31% of D. melanogaster genes, a 38% increase over previous estimations, but significantly less than that observed in higher organisms. Much of this splicing is subtle such as tandem alternate splice sites.

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“…Genes that showed reproducible reduction in their expression levels (ranging from 1.33-to 10-fold) in miR-31 transfectants were used for further analysis. Gene Ontology analysis of differentially expressed genes was performed using GeneCodis portal (21,22).…”

Section: Methodsmentioning

confidence: 99%

Pro-tumorigenic Effects of miR-31 Loss in Mesothelioma

Ivanov

Goparaju

Lopez

et al. 2010

Journal of Biological Chemistry

121

113

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The human genome encodes several hundred microRNA (miRNA) genes that produce small (21-23n) single strand regulatory RNA molecules. Although abnormal expression of miRNAs has been linked to cancer progression, the mechanisms of this dysregulation are poorly understood. Malignant mesothelioma (MM) of pleura is an aggressive and highly lethal cancer resistant to conventional therapies. We and others previously linked loss of the 9p21.3 chromosome in MM with short time to tumor recurrence. In this study, we report that MM cell lines derived from patients with more aggressive disease fail to express miR-31, a microRNA recently linked with suppression of breast cancer metastases. We further demonstrate that this loss is due to homozygous deletion of the miR-31-encoding gene that resides in 9p21.3. Functional assessment of miR-31 activity revealed its ability to inhibit proliferation, migration, invasion, and clonogenicity of MM cells. Re-introduction of miR-31 suppressed the cell cycle and inhibited expression of multiple factors involved in cooperative maintenance of DNA replication and cell cycle progression, including pro-survival phosphatase PPP6C, which was previously associated with chemotherapy and radiation therapy resistance, and maintenance of chromosomal stability. PPP6C, whose mRNA is distinguished with three miR-31-binding sites in its 3-untranslated region, was consistently down-regulated by miR-31 introduction and upregulated in clinical MM specimens as compared with matched normal tissues. Taken together, our data suggest that tumorsuppressive propensity of miR-31 can be used for development of new therapies against mesothelioma and other cancers that show loss of the 9p21.3 chromosome.

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GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists

Cited by 559 publications

References 26 publications

Proteomic differences in recombinant CHO cells producing two similar antibody fragments

Proteomic differences in recombinant CHO cells producing two similar antibody fragments

The Drosophila melanogaster transcriptome by paired-end RNA sequencing

Pro-tumorigenic Effects of miR-31 Loss in Mesothelioma

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