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From molecular activities and processes to biological function

J. van Helden
2001 Briefings in Bioinformatics  
A consortium of industries comprising Astra-Zeneca, Aventis, Monsanto, Organon and Roche has sponsored the work described here. Scientists from these companies are thanked for valuable input.  ...  We furthermore acknowledge support from the European Commission, Grant No, QLRI-CT-1999-01333.  ...  MARCH 2001 8 5 From molecular activities and processes to biological function Downloaded from https://academic.oup.com/bib/article-abstract/2/1/81/181010 by guest on 27 July 2018 & HENRY STEWART PUBLICATIONS  ... 
doi:10.1093/bib/2.1.81 pmid:11465065 fatcat:vo4wupziofdmlg6bskulkajtd4

A Description Scheme of Biological Processes Based on Elementary Bricks of Action

Pierre Mazière, Claude Granier, Franck Molina
2004 Journal of Molecular Biology  
Activities, Biological Functionalities and Biological Roles.  ...  With the fast growth of high-throughput strategies in Biology, there is a strong need to accelerate knowledge acquisition and organization of molecular functions.  ...  Acknowledgements We are indebted to Dr Sharon Lynn Salhi for editing the manuscript and Professor Marc Van Regenmortel, Dr Pierre Martineau and Dr Franc ¸ois Process Description Using Bricks of Action  ... 
doi:10.1016/j.jmb.2004.03.029 pmid:15123422 fatcat:37hle24aybdtzo3fwyuo6eebcy

The Gene Ontology and the Meaning of Biological Function [chapter]

Paul D. Thomas
2016 Msphere  
I then present an explicit formulation of the biological model that underlies the GO and annotations, and discuss how this model relates to the broader debates on the meaning of biological function.  ...  The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.  ...  Acknowledgments I want to thank Christophe Dessimoz, Pascale Gaudet, Jenna Hastings, and Ridhima Kad for helpful discussions on this topic, and for thoughtful reading and suggestions on the manuscript.  ... 
doi:10.1007/978-1-4939-3743-1_2 pmid:27812932 fatcat:meou26uuufes5efjkwpdm5v54e

Expression Analysis Systematic Explorer (EASE) analysis reveals differential gene expression in permanent and transient focal stroke rat models

Gregory Ford, Zhenfeng Xu, Alicia Gates, Ju Jiang, Byron D. Ford
2006 Brain Research  
However, EASE analysis of the regulated genes indicated molecular functions and biological processes unique to each model.  ...  These findings may give new insight to the molecular mechanisms involved in stroke and may lead to novel neuroprotective strategies. ava i l a b l e a t w w w. s c i e n c e d i r e c t . c o m w w w.  ...  The investigation was conducted in a facility constructed with support from Research Facilities Improvement Grant #C06 RR-07571 from the National Center for Research Resources, NIH.  ... 
doi:10.1016/j.brainres.2005.11.090 pmid:16409990 fatcat:k25o35sdarcihah7l6yhoc4w2e

Functional Analysis of the Aurora Kinase A Ile31 Allelic Variant in Human Prostate

Noa Matarasso, Anat Bar-Shira, Uri Rozovski, Serena Rosner, Avi Orr-Urtreger
2007 Neoplasia: An International Journal for Oncology Research  
When these hypothesis-generating results were subjected to more stringent statistical criteria, overexpression of a novel transcript of the natural killer tumor recognition sequence (NKTR) gene was revealed  ...  Significant overexpression of AURKA was demonstrated in homozygous and heterozygous AURKA Ile31 prostate RNA (2.07-fold and 1.93-fold, respectively; P < .05).  ...  We thank Merav Kedmi and Nicola Mabjeesh for their advice and support.  ... 
doi:10.1593/neo.07322 pmid:17898866 pmcid:PMC1993855 fatcat:llcpmsso5zaonfpul2q2lrk3wa

Identification of genomic regions associated with multi-silique trait in Brassica napus

Liang Chai, Jinfang Zhang, Kun Lu, Haojie Li, Lintao Wu, Hongshen Wan, Benchuan Zheng, Cheng Cui, Jun Jiang, Liangcai Jiang
2019 BMC Genomics  
Here, we combined bulked-segregant analysis (BSA) and whole genome re-sequencing (WGR) to map the genomic regions responsible for the multi-silique trait using two pools of DNA from the near-isogenic lines  ...  the molecular mechanism underlying this beneficial trait remains unclear.  ...  membrane (GO:0005886); Biological Process: proteolysis (GO:0006508); Biological Process: lipid transport (GO:0006869); Molecular Function: peptidase activity (GO:0008233); Molecular Function: lipid binding  ... 
doi:10.1186/s12864-019-5675-4 fatcat:yfzzjkr4xnbilmncnksghzxveq

Computing biological functions using BioΨ, a formal description of biological processes based on elementary bricks of actions

Sabine Pérès, Liza Felicori, Stéphanie Rialle, Elodie Jobard, Franck Molina
2010 Computer applications in the biosciences : CABIOS  
Results: We present a formalism that uses the Bio concepts to model biological processes from molecular details to networks.  ...  Motivation: In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult  ...  biological processes from sub-molecular details to networks.  ... 
doi:10.1093/bioinformatics/btq169 pmid:20448138 pmcid:PMC2881354 fatcat:6ndrnvoqvnbgtmcjaw5slftgjy

Characteristics of 292 Testis-Specific Genes in Human

Aifa Tang, Zhendong Yu, Yaoting Gui, Hui Zhu, Libin Zhang, Jianrong Zhang, Zhiming Cai
2007 Biological and Pharmaceutical Bulletin  
Of the 114 assigned, 63 are active in the molecular function, 28 genes in the cellular component, and 23 in the biological process, as shown in Table 2 .  ...  David GO was used for gene ontology with three main classes: biological process, cellular component, and molecular function. spermatogenesis and fertility.  ...  Using computational bioinformatics tools, 121 known testis-specific genes are grouped into three classes: cellular components, molecular function, and biological processes.  ... 
doi:10.1248/bpb.30.865 pmid:17473427 fatcat:jjyzzuarmrfihe3f4sr3u4wtnm

CERVICAL CANCER AND GENE EXPRESSION ANALYSIS WITH KEY GENES IDENTIFICATION BY COMPUTATIONAL METHOD

Swaminathan Venkataramnan, Wan Nurfazreen Binti Zainol Izam Khan
2020 Journal of Bio Innovation  
) continued in PANTHER (Protein Analysis Through Evolutionary Relationships database) for cervical cancer gene understanding through biological, molecular function to cellular level.  ...  Functional annotation analysis was conducted with a total of 247 gene list at Gene Expression Omnibus (GEO) database, then performed in DAVID (Database for Annotation, Visualization and Integrated Discovery  ...  The molecular function results showed 44.4% binding, 42.6% catalytic activity, 3.7% molecular function regulator, 5.6% molecular transducer activity and 3.7% structural molecule activity (Figure 3) .  ... 
doi:10.46344/jbino.2020.v09i05.26 fatcat:2cv2f27ffretlmmcyp7hf6xi7y

Emergence and Evolution of Modern Molecular Functions Inferred from Phylogenomic Analysis of Ontological Data

K. M. Kim, G. Caetano-Anolles
2010 Molecular biology and evolution  
The biological processes that characterize the phenotypes of a living system are embodied in the function of molecules and hold the key to evolutionary history, delimiting natural selection and change.  ...  These patterns unfold the metabolic origins of modern molecular functions and major biological transitions in evolution toward complex life.  ...  Any opinions, findings, and conclusions and recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies.  ... 
doi:10.1093/molbev/msq106 pmid:20418223 fatcat:clkp4duuurbmjko5efb4uq3trq

The bottom–up approach to defining life: deciphering the functional organization of biological cells via multi-objective representation of biological complexity from molecules to cells

Sathish Periyasamy, Alex Gray, Peter Kille
2013 Frontiers in Physiology  
activities contributing to functional organization, play a key role in cellular physiology.  ...  The paper proposes a multi-scale and multi-objective modeling approach from the bottom-up by representing temporally cohesive structures for multi-tasking of intracellular processes.  ...  The tasks/objectives range from being physical to chemical and biological, when traversing from molecular resolution to cellular resolution. At molecular resolution, the tasks are physical.  ... 
doi:10.3389/fphys.2013.00369 pmid:24385968 pmcid:PMC3866382 fatcat:up2kiydsuvhgfpx2oldelxhnqa

Comparison of Functional Gene Annotation of Toxascaris leonina and Toxocara canis using CLC Genomics Workbench

Ki Uk Kim, Sang Kyun Park, Shin Ae Kang, Mi Kyung Park, Min Kyoung Cho, Ho-jin Jung, Kyung-Yun Kim, Hak Sun Yu
2013 Korean Journal of Parasitology  
Overall, our results showed that most functional gene annotations of 2 ascarids were quite similar to each other in 3 major categories, i.e., cellular component, biological process, and molecular function  ...  A total of 2,880 and 7,949 ESTs were collected from T. leonina and T. canis, respectively. The length of ESTs ranged from 106 to 4,637 bp with an average insert size of 820 bp.  ...  Molecular function level 2 GO terms analyses of 3 organisms Biological process-related transcripts were classified according to 16 categories (antioxidant activity, binding, catalytic activity, cannel  ... 
doi:10.3347/kjp.2013.51.5.525 pmid:24327777 pmcid:PMC3857499 fatcat:dag6xwqupzcuji2q3r2nzqu4w4

Go molecular function terms are predictive of subcellular localization

Z Lu, L Hunter
2005 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Use of Gene Ontology (GO) molecular function terms to extend sequence-based subcellular localization prediction has been previously shown to improve predictive performance.  ...  Most predictive or informative terms are imperfect, and incorrect prediction may often call out significant biological phenomena. Finally, these results may be useful in the GO annotation process.  ...  Acknowledgments This work was supported by NIAAA grant 5U01 AA13524-03 (LH) and NIGMS graduate training grant T32-GM07635-25 (ZL).  ... 
pmid:15759622 pmcid:PMC2652875 fatcat:jgkqv7bgpbaivf7u4ydelld3be

GO MOLECULAR FUNCTION TERMS ARE PREDICTIVE OF SUBCELLULAR LOCALIZATION

Z. LU, L. HUNTER
2004 Biocomputing 2005  
Use of Gene Ontology (GO) molecular function terms to extend sequence-based subcellular localization prediction has been previously shown to improve predictive performance.  ...  Most predictive or informative terms are imperfect, and incorrect prediction may often call out significant biological phenomena. Finally, these results may be useful in the GO annotation process.  ...  Acknowledgments This work was supported by NIAAA grant 5U01 AA13524-03 (LH) and NIGMS graduate training grant T32-GM07635-25 (ZL).  ... 
doi:10.1142/9789812702456_0015 fatcat:3f3ib6loibgr5h2nw67rj3iywu

Gene Ontology annotations: what they mean and where they come from

David P Hill, Barry Smith, Monica S McAndrews-Hill, Judith A Blake
2008 BMC Bioinformatics  
annotation and ontology development and to more informed use of GO resources by experimental scientists. from 10 th Bio-Ontologies Special Interest Group Workshop 2007.  ...  Ten years past and looking to the future Vienna  ...  Acknowledgements The authors would like to thank Cynthia Smith, Terry Hayamizu and Waclaw Kusnierczyk, and the reviewers, for their help with this manuscript.  ... 
doi:10.1186/1471-2105-9-s5-s2 pmid:18460184 pmcid:PMC2367625 fatcat:kyqh4usdu5akfmsygvvrlcdkri
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