Bioinformatics Tools for Proteomics Data Interpretation

Calderón-González, Karla Grisel; Hernández-Monge, Jesús; Herrera-Aguirre, María Esther; Luna-Arias, Juan Pedro

doi:10.1007/978-3-319-41448-5_16

Cited by 26 publications

(14 citation statements)

References 50 publications

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“…Hierarchical clustering and PCA (principal component analysis) were carried out using ClustVis software (version 2.0) 38 . Functional assignments were generated using DAVID (database for annotation, visualization, and integrated discovery, v6.8) 39 and STRING 40 …”

Section: Methodsmentioning

confidence: 99%

Presumed cancer‐associated retinopathy (CAR) mimicking Sudden Acquired Retinal Degeneration Syndrome (SARDS) in canines

Grozdanić

Lazic

Kecova

et al. 2020

Veterinary Ophthalmology

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Objective To describe functional and structural features of presumed cancer‐associated retinopathy (CAR) mimicking sudden acquired retinal degeneration syndrome (SARDS) in dogs and describe treatment outcomes. Animals Subjects were 17 dogs from 8 eight US states and Canada diagnosed with SARDS or immune‐mediated retinitis (IMR) by 12 ophthalmologists. Nine eyes from seven deceased patients were used for microarray (MA), histology, or immunohistochemical (IHC) analysis. Procedures Dogs underwent complete ophthalmic examination, including retinal photography, optical coherence tomography (OCT), chromatic pupil light reflex testing (cPLR), and electroretinography (ERG), in addition to complete systemic examination. Histology, microarray, and IHC analysis were performed in CAR retinas to evaluate histological and molecular changes in retinal tissue. Results None of the patients evaluated satisfied previously established criteria for diagnosis of SARDS (flat ERG+ no red – good blue PLR), and all were diagnosed with IMR. All patients were diagnosed with a cancer: meningioma (24%), sarcoma (18%), pituitary tumor (12%), and squamous cell carcinoma (12%), other (34%). Median survival time was 6 months from diagnosis (range 1‐36 months). Most frequent systemic abnormalities were as follows: proteinuria (78%); elevated liver enzymes (47%); and metabolic changes (PU/PD, polyphagia – 24%). Immunosuppressive therapy resulted in the reversal of blindness in 44% of treated patients, with 61% of all treated patients recovering and/or maintaining vision. Median time for preservation of vision was 5 months (range 1‐35 months). Conclusions Observed changes are highly suggestive of immune‐mediated damage in IMR‐CAR eyes. A relatively high percentage of patients with CAR responded positively to immunosuppressive therapy.

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Section: Methodsmentioning

confidence: 99%

Presumed cancer‐associated retinopathy (CAR) mimicking Sudden Acquired Retinal Degeneration Syndrome (SARDS) in canines

Grozdanić

Lazic

Kecova

et al. 2020

Veterinary Ophthalmology

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“…DAVID 6.7 (), an online open platform that disseminates biologically abundant information across a comprehensive analysis of large gene lists, was used for clustering analysis (30). Potential target genes were searched in the annotated portal DAVID.…”

Section: Methodsmentioning

confidence: 99%

Prognostic value and prospective molecular mechanism of miR‑100‑5p in hepatocellular carcinoma: A comprehensive study based on 1,258 samples

Qin

Lin

et al. 2019

Oncol Lett

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The prognostic value and molecular mechanism of microRNA-100-5p (miR-100-5p) in hepatocellular carcinoma (HCC) are still unclear. To explore the prognostic value and the mechanism of miR-100-5p in HCC, the present study analyzed the results of 18 previous studies and bioinformatic datasets. The clinical significance of miR-100-5p and its targets in HCC were investigated using The Cancer Genome Atlas and the Gene Expression Omnibus, as well as relevant literature. In total, 12 online tools were used to predict the target genes of miR-100-5p. Bioinformatics analysis and Spearman correlation analysis were performed, and genomic alterations of the hub genes were evaluated. A meta-analysis with 1,258 samples revealed that miR-100-5p was significantly downregulated in HCC [standard mean difference (SMD), −0.94; 95% confidence interval (CI), −1.14 to −0.74; I2, 35.2%]. Lower miR-100-5p expression was associated with poorer clinical characteristics and a poorer prognosis for patients with HCC. Additionally, bioinformatics analysis revealed that the ‘regulation of transcription’, ‘chromatin remodeling complex’, ‘transcription regulator activity’, ‘pathways in cancer’ and ‘heparan sulfate biosynthesis’ were the most enriched terms. Furthermore, expression of histone deacetylase (HDAC)2, HDAC3, SHC-transforming protein 1 (SHC1), Ras-related protein Rac1 (RAC1) and E3 ubiquitin-protein ligase CBL (CBL) was negatively correlated with miR-100-5p expression. Among these, upregulated HDAC2 [hazard ratio (HR), 1.910; 95% CI, 1.309–2.787; P=0.0007], HDAC3 (HR, 1.474; 95% CI, 1.012–2.146; P=0.0435), SHC1 (HR, 1.52; 95% CI, 1.043–2.215; P=0.0281) and RAC1 (HR, 1.817; 95% CI, 1.248–2.645; P=0.0022) were associated with shorter survival. Alterations in HDAC2, SHC1, RAC1 and IGF1R were linked with a poorer outcome for HCC, and alternative splicing of SHC and RAC1 were significantly decreased and increased in HCC, respectively. In summary, the downregulation of miR-100-5p may be involved in the progression and prognosis of HCC. The upregulation of HDAC2, HDAC3, SHC1 and RAC1 may indicate a poorer survival rate for patients with HCC. Thus, miR-100-5p and these 4 potential target genes may provide novel therapeutic targets and prognostic predictors for patients with HCC.

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“…Applications may include determining the localization of identified proteins and characterizing biological processes, signaling pathways in which they are involved and possible interactions that bind the different proteins, as well as streamlining potential new physiological mechanisms. More information on open source bioinformatics tools can be found in [2].…”

Section: Figurementioning

confidence: 99%

The Human Ovary and Future of Fertility Assessment in the Post-Genome Era

Ouni

Vertommen

Amorim

2019

IJMS

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Proteomics has opened up new avenues in the field of gynecology in the post-genome era, making it possible to meet patient needs more effectively and improve their care. This mini-review aims to reveal the scope of proteomic applications through an overview of the technique and its applications in assisted procreation. Some of the latest technologies in this field are described in order to better understand the perspectives of its clinical applications. Proteomics seems destined for a promising future in gynecology, more particularly in relation to the ovary. Nevertheless, we know that reproductive biology proteomics is still in its infancy and major technical and ethical challenges must first be overcome.

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Bioinformatics Tools for Proteomics Data Interpretation

Cited by 26 publications

References 50 publications

Presumed cancer‐associated retinopathy (CAR) mimicking Sudden Acquired Retinal Degeneration Syndrome (SARDS) in canines

Presumed cancer‐associated retinopathy (CAR) mimicking Sudden Acquired Retinal Degeneration Syndrome (SARDS) in canines

Prognostic value and prospective molecular mechanism of miR‑100‑5p in hepatocellular carcinoma: A comprehensive study based on 1,258 samples

The Human Ovary and Future of Fertility Assessment in the Post-Genome Era

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