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Quality controls in integrative approaches to detect errors and inconsistencies in biological databases

Giorgio Ghisalberti, Marco Masseroli, Luca Tettamanti
2010 Journal of Integrative Bioinformatics  
It allows comprehensive statistical analysis and mining of functional and phenotypic annotations of gene lists, such as those identified by high-throughput biomolecular experiments.  ...  This makes it the most suitable also to implement comprehensive quality controls on integrated data.  ...  of the analysis performed on them (e.g. the enrichment analysis of gene expression experiment results).  ... 
doi:10.2390/biecoll-jib-2010-119 pmid:20375464 fatcat:za4v2ehq2jhkfhsnha6naysxxa

Quality controls in integrative approaches to detect errors and inconsistencies in biological databases

Giorgio Ghisalberti, Marco Masseroli, Luca Tettamanti
2010 Journal of Integrative Bioinformatics  
It allows comprehensive statistical analysis and mining of functional and phenotypic annotations of gene lists, such as those identified by high-throughput biomolecular experiments.  ...  This makes it the most suitable also to implement comprehensive quality controls on integrated data.  ...  of the analysis performed on them (e.g. the enrichment analysis of gene expression experiment results).  ... 
doi:10.1515/jib-2010-119 fatcat:xtbsy7awqfgzra2jlcfysyqmiy

Quality Control of Expression Profiling Data

Mikhail Soloviev
2015 Journal of Proteomics & Bioinformatics  
Acknowledgements ATM carried out the experimental work and contributed to the drafting of the manuscript. MS conceived and supervised the study, and drafted the manuscript.  ...  and suitability of the data for gene expression analysis.  ...  Introduction mRNA expression profiling is now well established and a number of techniques are employed for acquiring and analysis of data on a sample's transcriptome or for studying differential gene expression  ... 
doi:10.4172/jpb.1000366 fatcat:ul4vs6yb2vablf3il7r6ujfsz4

maGUI: A Graphical User Interface for Analysis and Annotation of DNA Microarray Data

Dhammapal Bharne, Praveen Kant, Vaibhav Vindal
2019 The Open Bioinformatics Journal  
The user may proceed from loading of microarray data to normalization, quality check, filtering, differential gene expression, principal component analysis, clustering and classification.  ...  Further, the user can build a co-expression network for differentially expressed genes. Tables and figures generated during the analysis can be viewed and exported to local disks.  ...  ACKNOWLEDGEMENTS Authors would like to thank funding support from DST-PURSE, UPE to Department of Biotechnology and Bioinformatics, University of Hyderabad. DB is supported by UGC fellowship.  ... 
doi:10.2174/1875036201912010040 fatcat:2ube525aprcunbe2y27hloyjce

Hybrid Integration of Molecular-Biological Annotation Data [chapter]

Toralf Kirsten, Hong-Hai Do, Christine Körner, Erhard Rahm
2005 Lecture Notes in Computer Science  
We present a new approach to integrate annotation data from public sources for the expression analysis of genes and proteins.  ...  This hybrid integration approach has been implemented for a large gene expression warehouse and supports functional analysis using annotation data from GeneOntology, Locuslink and Ensembl.  ...  Conclusions We presented a hybrid approach for the integration of annotation data from public data sources to support expression analysis of genes and proteins.  ... 
doi:10.1007/11530084_17 fatcat:q6cabiw2ivc3vp4awao2yn7kh4

Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data

Antonio Federico, Angela Serra, My Kieu Ha, Pekka Kohonen, Jang-Sik Choi, Irene Liampa, Penny Nymark, Natasha Sanabria, Luca Cattelani, Michele Fratello, Pia Anneli Sofia Kinaret, Karolina Jagiello (+8 others)
2020 Nanomaterials  
Moreover, we discuss the most common methods for the identification of differentially expressed genes and to perform a functional enrichment analysis.  ...  of the mechanism of action (MOA) of different compounds.  ...  Acknowledgments: The authors would like to thank David Winkler for critical comments to the manuscript. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/nano10050903 pmid:32397130 pmcid:PMC7279140 fatcat:tjufrgpek5dldluw4egoc2wg7m

Gene Expression Data Management: A Case Study [chapter]

Victor M. Markowitz, I-Min A. Chen, Anthony Kosky
2002 Lecture Notes in Computer Science  
One of the major challenges facing scientists dealing with gene expression data is how to integrate, explore and analyze vast quantities of  ...  We want to thank our colleagues at Gene Logic who have been involved in the development of the GeneExpress system for their outstanding work.  ...  Special thanks to Mike Cariaso and Krishna Palaniappan for their contributions to this paper.  ... 
doi:10.1007/3-540-45876-x_45 fatcat:5vbrsag5gfgrtmvzifdcumarn4

Visualization of High Throughput Genomic Data Using R and Bioconductor

Ruchi Yadav, Prachi Srivastava
2016 Journal of Data Mining in Genomics & Proteomics  
One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project for the analysis and comprehension of genomic data, based on the R programming  ...  Computational analysis plays an important part related to the processing of the biological information embedded in microarray results and for comparing gene expression result obtained from different samples  ...  Acknowledgements This is not just to follow the custom of writing acknowledgement but to express and record my heart felt feeling of thankfulness to all those who directly or indirectly helped me in this  ... 
doi:10.4172/2153-0602.1000197 fatcat:mq46qludmbbnnkgrc4irttqfyy

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Frederic B Bastian, Julien Roux, Anne Niknejad, Aurélie Comte, Sara S Fonseca Costa, Tarcisio Mendes de Farias, Sébastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki (+11 others)
2020 Nucleic Acids Research  
Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or  ...  It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression.  ...  of data to annotate and for use-cases.  ... 
doi:10.1093/nar/gkaa793 pmid:33037820 pmcid:PMC7778977 fatcat:rmkspvb7v5ae3dfpti3p5riyfy

MERAV: a tool for comparing gene expression across human tissues and cell types

Yoav D. Shaul, Bingbing Yuan, Prathapan Thiru, Andy Nutter-Upham, Scott McCallum, Carolyn Lanzkron, George W. Bell, David M. Sabatini
2015 Nucleic Acids Research  
MERAV has been designed as a powerful tool for whole genome analysis which offers multiple advantages: one can search many genes in parallel; compare gene expression among different tissue types as well  ...  We have recently demonstrated essential metabolic processes in tumor progression through the development of a methodological analysis of gene expression.  ...  ACKNOWLEDGEMENT We want to thank Eric Hagman, Brad Wilson and Logan Engstrom for their help in initiating the website; Michael Pacold for suggesting the name MERAV; and members of the Sabatini lab for  ... 
doi:10.1093/nar/gkv1337 pmid:26626150 pmcid:PMC4702927 fatcat:hahkdf23tjh2vpaugysm5pbg3a

SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis [article]

Samuel Blanck, Guillemette Marot
2018 arXiv   pre-print
Conclusion: The use of Galaxy offers an easy-to-use gene expression meta-analysis tool suite based on the metaMA and metaRNASeq packages.  ...  Results: SMAGEXP (Statistical Meta-Analysis for Gene EXPression) integrates metaMA and metaRNAseq packages into Galaxy.  ...  As for the limma tool, annotated expressed genes are displayed in a table which can be ordered and requested.  ... 
arXiv:1802.08251v1 fatcat:3kfbizpjj5cotgn6y52wswz2ry

Identification and Functional Prediction of Circular RNAs Related to Growth Traits and Skeletal Muscle Development in Duroc pigs

Lixia Ma, Wei Chen, Shiyin Li, Ming Qin, Yongqing Zeng
2022 Frontiers in Genetics  
Most of the DE circRNAs were enriched in Quantitative trait locus (QTL) regions related to meat quality and growth traits. In addition, a gene can produce one or more circRNA transcripts.  ...  It was also found that the source genes of DE circRNAs were enriched in MAPK, FoXO, mTOR, PI3K-Akt, and Wnt signaling pathways.  ...  Different colors represent the different number of source genes. For instance, blue represents the number of source genes that produce one circRNA transcript.  ... 
doi:10.3389/fgene.2022.858763 pmid:36118900 pmcid:PMC9478749 fatcat:vzus5nddevfk3aglftc67eiwoa

CRISP-view: a database of functional genetic screens spanning multiple phenotypes

Yingbo Cui, Xiaolong Cheng, Qing Chen, Bicna Song, Anthony Chiu, Yuan Gao, Tyson Dawson, Lumen Chao, Wubing Zhang, Dian Li, Zexiang Zeng, Jijun Yu (+4 others)
2020 Nucleic Acids Research  
The rapid accumulation of public available genetic screening data provides a wealth of knowledge about genotype-to-phenotype relationships and a valuable resource for the systematic analysis of gene functions  ...  All the datasets have been curated, annotated, and processed by a standard MAGeCK-VISPR analysis pipeline with quality control (QC) metrics.  ...  ACKNOWLEDGEMENTS The authors would like to thank Jingyu Peng, Shengqing Gu, Feizheng Wu for the helpful discussion about the project, and Johannes Köster for the help of developing the visualization module  ... 
doi:10.1093/nar/gkaa809 pmid:33010154 fatcat:qx5gn3zxxvaadhahnm32to5c5m

Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica

G.-Z. Wu, Q.-M. Shi, Y. Niu, M.-Q. Xing, H.-W. Xue
2007 Nucleic Acids Research  
The RAPESEED includes the resource of 8462 unique ESTs, of which 3526 clones are with full length cDNA; the expression profiles of 8095 genes and the Serial Analysis of Gene Expression (SAGE, 23 895 unique  ...  The Shanghai RAPESEED Database (RAPESEED, http://rapeseed.plantsignal.cn/) was created to provide the solid platform for functional genomics studies of oilseed crops with the emphasis on seed development  ...  We thank Liang-Jiao Xue for his help with the database construction. Funding to pay the Open Access publication charges for this article was provided by 2006CB101603.  ... 
doi:10.1093/nar/gkm780 pmid:17916574 pmcid:PMC2238842 fatcat:jqhd6re5bfcwvptnwdtjyk5oyu

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

Robin P Smith, William J Buchser, Marcus B Lemmon, Jose R Pardinas, John L Bixby, Vance P Lemmon
2008 BMC Bioinformatics  
The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter  ...  of seconds.  ...  Khuri for critical comments on the manuscript.  ... 
doi:10.1186/1471-2105-9-186 pmid:18402700 pmcid:PMC2322989 fatcat:bcfwozbvjbbixagfi4agm2gdnm
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