PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

Barbosa-Silva, Adriano; Fontaine, Jean-Fred; Donnard, Elisa; Stussi, Fernanda; Ortega, Josè Miguel; Andrade‐Navarro, Miguel A.

doi:10.1186/1471-2105-12-435

Cited by 44 publications

(35 citation statements)

References 40 publications

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“…We thus performed biointeraction analysis to detect the regulating networks of these SG genes using the text-mining approach, PESCADOR (35). (Details in Supplementary Methods and Results and Supplementary Figure S4.…”

Section: Resultsmentioning

confidence: 99%

SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining

Zhang¹,

Zhong²,

Xu³

et al. 2012

Nucleic Acids Research

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Human infertility affects 10–15% of couples, half of which is attributed to the male partner. Abnormal spermatogenesis is a major cause of male infertility. Characterizing the genes involved in spermatogenesis is fundamental to understand the mechanisms underlying this biological process and in developing treatments for male infertility. Although many genes have been implicated in spermatogenesis, no dedicated bioinformatic resource for spermatogenesis is available. We have developed such a database, SpermatogenesisOnline 1.0 (http://mcg.ustc.edu.cn/sdap1/spermgenes/), using manual curation from 30 233 articles published before 1 May 2012. It provides detailed information for 1666 genes reported to participate in spermatogenesis in 37 organisms. Based on the analysis of these genes, we developed an algorithm, Greed AUC Stepwise (GAS) model, which predicted 762 genes to participate in spermatogenesis (GAS probability >0.5) based on genome-wide transcriptional data in Mus musculus testis from the ArrayExpress database. These predicted and experimentally verified genes were annotated, with several identical spermatogenesis-related GO terms being enriched for both classes. Furthermore, protein–protein interaction analysis indicates direct interactions of predicted genes with the experimentally verified ones, which supports the reliability of GAS. The strategy (manual curation and data mining) used to develop SpermatogenesisOnline 1.0 can be easily extended to other biological processes.

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Section: Resultsmentioning

confidence: 99%

SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining

Zhang¹,

Zhong²,

Xu³

et al. 2012

Nucleic Acids Research

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“…Thus, PESCADOR allows selecting gene-protein co-occurrence pairs based on their relatedness to biological concepts and therefore brings together under a common perspective protein interactions that have not been studied under the same research focus [ 13 ] .…”

Section: The Use Of a Systems Biology Approach To Better Understand Tmentioning

confidence: 99%

“…PESCADOR uses LAITOR-Literature Assistant for Identi fi cation of Terms coOccurrences and Relationships as text-mining engine to extract sentences with cooccurring bioentities (genes and proteins) from the text of the PubMed abstracts requested [ 13 ] . Thus, PESCADOR allows selecting gene-protein co-occurrence pairs based on their relatedness to biological concepts and therefore brings together under a common perspective protein interactions that have not been studied under the same research focus [ 13 ] .…”

Section: The Use Of a Systems Biology Approach To Better Understand Tmentioning

confidence: 99%

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Chronobiology and Metabolic Syndrome: From Genes to Systems Biology

Sookoian

Pirola

2012

Chronobiology and Obesity

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The major function of the circadian system is the internal cycling of physiologic and metabolic events. In the last years, there has been an exponential increase in our understanding of the role of clock-related genes in Metabolicsyndrome (MetS)-related phenotypes. Nevertheless, our understanding about how the components of the circadian system interact each other to modulate the metabolism and cardiovascular system remains a major challenge.Systems biology introduces a new concept for revealing the pathogenesis of human disorders and suggests the presence of common physiologic processes and molecular networks in fl uencing the risk of a disease. In this review, we use systems biology approaches to integrate genomic, molecular, and physiological data to decipher putative circadian rhythmic pathways suspected to play a role in the etiology of the metabolic syndrome (MetS)-associated phenotypes with a main focus in obesity and as other authors are discussing diverse related topics, we discuss the fi ndings of our own group.

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“…Therefore, we used the Platform for Exploration of Significant Concepts Associated to Co-occurrences Relationships (PESCADOR) (9) with the query "(fetal programming OR newborn body weight OR small for gestational age OR SGA OR large for gestational age) and (epigenetics OR DNA methylation or histone). " PESCADOR allows the selection of gene/protein co-occurrence pairs based on their relatedness to biological concepts, bringing together, under a common perspective, protein interactions that have not been studied under the same research focus (9). After abstract tagging, 699 gene/ protein terms were identified in 942 published abstracts.…”

Section: Reviewmentioning

confidence: 99%

Fetal metabolic programming and epigenetic modifications: a systems biology approach

et al. 2013

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A growing body of evidence supports the notion that epigenetic changes such as DNA methylation and histone modifications, both involving chromatin remodeling, contribute to fetal metabolic programming. We use a combination of gene-protein enrichment analysis resources along with functional annotations and protein interaction networks for an integrative approach to understanding the mechanisms underlying fetal metabolic programming. systems biology approaches suggested that fetal adaptation to an impaired nutritional environment presumes profound changes in gene expression that involve regulation of tissue-specific patterns of methylated cytosine residues, modulation of the histone acetylation-deacetylation switch, cell differentiation, and stem cell pluripotency. The hypothalamus and the liver seem to be differently involved. In addition, new putative explanations have emerged about the question of whether in utero overnutrition modulates fetal metabolic programming in the same fashion as that of a maternal environment of undernutrition, suggesting that the mechanisms behind these two fetal nutritional imbalances are different. In conclusion, intrauterine growth restriction is most likely to be associated with the induction of persistent changes in tissue structure and functionality. conversely, a maternal obesogenic environment is most probably associated with metabolic reprogramming of glucose and lipid metabolism, as well as future risk of metabolic syndrome (Ms), fatty liver, and insulin (INs) resistance.L arge amounts of epidemiological data showed that impaired intrauterine growth and adult metabolic and cardiovascular disorders, including coronary heart disease, type 2 diabetes, and insulin (INS) resistance, are strongly associated (1-4). Actually, the first exploration of a putative connection between environmental influence in early life and the risk of cardiovascular disease in adulthood was done by David Barker and coworkers, who followed-up a cohort of 499 men and women born in Preston (Lancashire, UK) during 1935-1943, and observed that as adults the highest blood pressures occurred in people who had been small babies with large placentas (5).Of note, the concept of a relationship between birth weight and adult chronic diseases initially described in low-birthweight babies was further extended to large-for-gestational age (LGA) babies, and the term of inappropriate gestational weight gained acceptance to better illustrate changes in earlylife metabolic environment that contribute to the risk of metabolic syndrome (MS) in adulthood (6).Barker and Hales also provided the initial answer to the question of how birth weight and adult chronic diseases are connected. They explained that fetuses adapt to an impaired supply of nutrients by changing their physiology and metabolism, and altering the sensitivity of tissues causes an abnormal structure and function in adult life; thereby, they formulated the "thrifty phenotype hypothesis" (7,8).Altogether, the above-mentioned clinico-epidemiological evidence str...

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PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

Cited by 44 publications

References 40 publications

SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining

SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining

Chronobiology and Metabolic Syndrome: From Genes to Systems Biology

Fetal metabolic programming and epigenetic modifications: a systems biology approach

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