GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

Nogales-Cadenas, Rubén; Carmona-Sáez, Pedro; Vázquez, Miguél; Vicente, Cesar; Yang, Xiaoyuan; Tirado, Francisco; Carazo, José Marı́a; Pascual-Montano, Alberto

doi:10.1093/nar/gkp416

Cited by 402 publications

(292 citation statements)

References 17 publications

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“…Tumor suppressive microRNAs in prostate cancer M Fuse et al PCa cells, we conducted a GeneCodis analysis 40 of our miR-222 or miR-31 transfectant expression profiles. The GeneCodis analysis applies many genes to known pathways in KEGG, 41 and these data facilitate understanding of tumor suppressive, miRNA-regulated molecular networks in cancer.…”

Section: Discussionmentioning

confidence: 99%

Tumor suppressive microRNAs (miR-222 and miR-31) regulate molecular pathways based on microRNA expression signature in prostate cancer

et al. 2012

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microRNAs (miRNAs) have key roles in human tumorigenesis, tumor progression and metastasis. miRNAs are aberrantly expressed in many human cancers and can function as tumor suppressors or oncogenes that target many cancer-related genes. This study seeks to identify novel miRNA-regulated molecular pathways in prostate cancer (PCa). The miRNA expression signature in clinical specimens of PCa showed that 56 miRNAs were significantly downregulated in PCa compared with nonPCa tissues. We focused on the top four downregulated miRNAs (miR-187, miR-205, miR-222 and miR-31) to investigate their functional significance in PCa cells. Expression levels of these four miRNAs were validated in PCa specimens (15 PCa tissues and 17 non-PCa tissues) to confirm that they were significantly reduced in these PCa tissues. Gain-of-function analysis demonstrated that miR-222 and miR-31 inhibited cell proliferation, invasion and migration in PCa cell lines (PC3 and DU145), suggesting that miR-222 and miR-31 may act as tumor suppressors in PCa. Genome-wide gene expression analysis using miR-222 or miR-31 transfectants to identify the pathways they affect showed that many cancer-related genes are regulated by these miRNAs in PC3 cells. Identification and categorization of the molecular pathways regulated by tumor suppressive miRNAs could provide new information about the molecular mechanisms of PCa tumorigenesis.

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Section: Discussionmentioning

confidence: 99%

Tumor suppressive microRNAs (miR-222 and miR-31) regulate molecular pathways based on microRNA expression signature in prostate cancer

et al. 2012

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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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“…To assess whether any particular gene classes were specifically enriched for dsRBDdependent Stau1 binding, we performed gene ontology analysis using GeneCodis [27][28][29] (Supplementary Table 3). We obtained the most significant associations for the 469 genes having the highest WT/mut CDS cross-linking ratios (>1.9) and the 515 genes exhibiting high WT cross-linking to strongly distal 3′ UTRs.…”

Section: Gene Ontology Analysismentioning

confidence: 99%

Staufen1 senses overall transcript secondary structure to regulate translation

Ricci

Küçükural

Cenik

et al. 2013

Nat Struct Mol Biol

122

184

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Human Staufen1 (Stau1) is a double-stranded RNA (dsRNA)-binding protein implicated in multiple post-transcriptional gene-regulatory processes. Here we combined RNA immunoprecipitation in tandem (RIPiT) with RNase footprinting, formaldehyde cross-linking, sonication-mediated RNA fragmentation and deep sequencing to map Staufen1-binding sites transcriptome wide. We find that Stau1 binds complex secondary structures containing multiple short helices, many of which are formed by inverted Alu elements in annotated 3′ untranslated regions (UTRs) or in 'strongly distal' 3′ UTRs. Stau1 also interacts with actively translating ribosomes and with mRNA coding sequences (CDSs) and 3′ UTRs in proportion to their GC content and propensity to form internal secondary structure. On mRNAs with high CDS GC content, higher Stau1 levels lead to greater ribosome densities, thus suggesting a general role for Stau1 in modulating translation elongation through structured CDS regions. Our results also indicate that Stau1 regulates translation of transcription-regulatory proteins.Staufen proteins are highly conserved dsRNA-binding proteins (dsRBPs) found in most bilateral animals 1 . Mammals contain two Staufen paralogs encoded by different loci. Stau1, Reprints and permissions information is available online at

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GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

Cited by 402 publications

References 17 publications

Tumor suppressive microRNAs (miR-222 and miR-31) regulate molecular pathways based on microRNA expression signature in prostate cancer

Tumor suppressive microRNAs (miR-222 and miR-31) regulate molecular pathways based on microRNA expression signature in prostate cancer

Proteomic differences in recombinant CHO cells producing two similar antibody fragments

Staufen1 senses overall transcript secondary structure to regulate translation

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