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GeneLynx specifications

Information


Unique identifier OMICS_25505
Name GeneLynx
Restrictions to use Academic or non-commercial use
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained No

Publication for GeneLynx

GeneLynx citations

 (6)
call_split

Neuroadaptations in Human Chronic Alcoholics: Dysregulation of the NF κB System

2007
PLoS One
PMCID: 1976556
PMID: 17895971
DOI: 10.1371/journal.pone.0000930
call_split See protocol

[…] (TFBS) were identified in phylogenetically conserved (human versus rat) regions of the 10 kb-promoter region. The weight matrices for TFBS identification were taken from JASPAR . Prometheus uses the GeneLynx Database and the GeneLynx application programming interface to obtain the genomic coordinates and sequences for human and rat species with an upstream promoter length of 10 kb. LAGAN aligner […]

library_books

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

2006
Malar J
PMCID: 1665468
PMID: 17112376
DOI: 10.1186/1475-2875-5-110

[…] le software for local analyses are strongly needed.Various tools aim to provide biological interpretation of gene clusters but these mostly specialize in only one or two types of analyses. FatiGO [], GeneLynx [] and Gostat [] are powerful tools for Gene Ontology mining; GoMiner [], MAPPFinder [] and DAVID [] use GO and metabolic pathway interpretation whereas GeneXPress [] and MiCoViTo [] use meta […]

library_books

NovelFam3000 – Uncharacterized human protein domains conserved across model organisms

2006
BMC Genomics
PMCID: 1440326
PMID: 16533400
DOI: 10.1186/1471-2164-7-48

[…] vided via a "gene page". Organism-centric resource links for each gene include WormBase [], Flybase [], and SGD []. For human proteins, links are provided to genome browsers [,] and the meta-database GeneLynx []. For each protein, we provide links to the Biomolecular Interaction Network Database (BIND) [], as well as to the Interolog Analysis system Ulysses [,] that displays protein-protein intera […]

library_books

Exploring hepatic hormone actions using a compilation of gene expression profiles

2005
PMCID: 1180834
PMID: 15953391
DOI: 10.1186/1472-6793-5-8

[…] for mouse cDNA sequences aligning to the same loci as the rat sequences and indicating similar gene structures. Human cDNA sequences orthologous to the mouse cDNA sequences were identified using the GeneLynx database [,]. Guided by genomic mappings of the cDNA sequences from the UCSC Genome Browser Database [], we retrieved human (NCBI build 33) and mouse gene and promoter sequences. Since cDNA s […]

call_split

A combined approach exploring gene function based on Worm Human Orthology

2005
BMC Genomics
PMCID: 1112593
PMID: 15877817
DOI: 10.1186/1471-2164-6-65
call_split See protocol

[…] In order to select candidate genes for the RNAi experiments phylogenetic reconstructions were performed as follows: C. elegans and related sequences were collected from Genelynx or/and Wormbase . The data set typically included several homologs of the model organisms (yeast, fly, etc.) and one or more human sequences. Multiple sequences alignments were done using Cl […]

call_split

Identification of functional SNPs in the 5 prime flanking sequences of human genes

2005
BMC Genomics
PMCID: 550646
PMID: 15717931
DOI: 10.1186/1471-2164-6-18
call_split See protocol

[…] mic mapping with the highest number of matching bases. Orthologous mouse loci were identified by similarly retrieving mouse genomic mappings for mouse cDNAs defined as orthologs to the human cDNAs in GeneLynx []. To more reliably identify transcriptional start sites we searched for other cDNA mappings overlapping the retrieved mappings and indicating similar gene structures. For each gene, the cDN […]

Citations

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GeneLynx institution(s)
Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden; Bioinformatics Unit, PA, USA; Pharmacia Corporation, Stockholm, Sweden
GeneLynx funding source(s)
Supported by funds from the Karolinska Institute and the Pharmacia Corporation.

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