Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges

Jorge, Natasha Andressa Nogueira; Ferreira, Carlos Gil; Passetti, Fábio

doi:10.3389/fgene.2012.00287

Cited by 11 publications

(7 citation statements)

References 130 publications

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“…More specifically, complete analytical pipelines for noncoding RNAs (ncRNAs) are also needed, as aberrant patterns in (very) long and noncoding RNAs have been explored as important biomarkers for the classification of subtypes of cancers and other diseases, as primary factors in oncogenesis, and for therapeutic effects 69,71,72,76 .…”

Section: Discussionmentioning

confidence: 99%

Temporal dynamics in meta longitudinal RNA-Seq data

Baldwin

et al. 2019

Sci Rep

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Identification of differentially expressed genes has been a high priority task of downstream analyses to further advances in biomedical research. Investigators have been faced with an array of issues in dealing with more complicated experiments and metadata, including batch effects, normalization, temporal dynamics (temporally differential expression), and isoform diversity (isoform-level quantification and differential splicing events). To date, there are currently no standard approaches to precisely and efficiently analyze these moderate or large-scale experimental designs, especially with combined metadata. In this report, we propose comprehensive analytical pipelines to precisely characterize temporal dynamics in differential expression of genes and other genomic features, i.e., the variability of transcripts, isoforms and exons, by controlling batch effects and other nuisance factors that could have significant confounding effects on the main effects of interest in comparative models and may result in misleading interpretations.

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Section: Discussionmentioning

confidence: 99%

Temporal dynamics in meta longitudinal RNA-Seq data

Baldwin

et al. 2019

Sci Rep

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“…For example, RNA-Seq enabled the discovery of new potential splice isoforms [8,9] and the analysis of transcript expression levels [10] in different cell types and conditions. The methods of sequencing and the assembly of reads have been compared [11] and improved over the past few years, promoting new perspectives in transcriptomics [12], including noncoding RNAs (reviewed in [13]). …”

Section: Introductionmentioning

confidence: 99%

Splice variants in the proteome: a promising and challenging field to targeted drug discovery

Tavares

Scherer

Ferreira

et al. 2015

Drug Discovery Today

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“…With the progress and development of biotechnology such as genome sequencing, it has been confirmed that more than 97% of the transcripts in the human genome do not have the function of coding protein, that is, non-coding RNA (ncRNA), which mainly includes small non-coding RNA (miRNA) and long non-coding RNA(lncRNA) [ 3 ]. MiRNAs generally have 18 to 25 nucleotides, and their sequences are highly conserved in evolution.…”

Section: Introductionmentioning

confidence: 99%

LncRNA GACAT1 targeting miRNA-149 regulates the molecular mechanism of proliferation, apoptosis and autophagy of oral squamous cell carcinoma cells

Chen

et al. 2021

Aging

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To explore the effects of lncRNA GACAT1/miR-149 molecular axis on the proliferation, apoptosis, migration and autophagy of oral squamous cell carcinoma (OSCC) cells, and to explore its molecular mechanism. The expressions of lncRNA GACAT1 and miR-149 in tissues and cell lines of patients with OSCC were detected by qRT-PCR. Si-control, GACAT1-siRNA, inhibitor NC and miR-149 inhibitors were transfected into OSCC cells separately or in combination with Lipofectamine 2000. The binding sites between lncRNA GACAT1 and miR-149 were predicted using the miRanda website, and the targeting relationship was verified by dual-luciferase assay. The expression of lncRNA XIST and miR-149 was detected by qRT-PCR. CCK-8 assay was used to detect cell activity. Cell cycle distribution and apoptosis were detected by flow cytometry. Cell migration ability was detected by Transwell assay. The expression of migration and autophagy-related proteins was detected by western blot. LncRNA GACAT1 was highly expressed in cancer tissues and cell lines of OSCC patients ( P < 0.01), while miR-149 was low expressed ( P < 0.01). LncRNA GACAT1 binds to miR-149 targeting. The down-regulation of lncRNA GACAT1 inhibited the proliferation and migration of OSCC cells and promoted apoptosis and autophagy ( P < 0.01). The transfection of miR-149 inhibitor had the opposite effect. Knockdown of lncRNA GACAT1 and transfection with miR-149 inhibitor reversed the effect of GACAT1 silencing on OSCC cells. Inhibition of lncRNA GACAT1 can inhibit the proliferation and migration of OSCC cells, promote apoptosis and autophagy, and the mechanism may be related to the targeting of miR-149.

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Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges

Cited by 11 publications

References 130 publications

Temporal dynamics in meta longitudinal RNA-Seq data

Temporal dynamics in meta longitudinal RNA-Seq data

Splice variants in the proteome: a promising and challenging field to targeted drug discovery

LncRNA GACAT1 targeting miRNA-149 regulates the molecular mechanism of proliferation, apoptosis and autophagy of oral squamous cell carcinoma cells

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