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|Restrictions to use||Academic or non-commercial use|
|Database management system||MySQL|
|Data access||File download, Browse|
|User data submission||Allowed|
Publication for GeneLynx
Neuroadaptations in Human Chronic Alcoholics: Dysregulation of the NF κB System
[…] (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 […]
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
[…] 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 […]
NovelFam3000 – Uncharacterized human protein domains conserved across model organisms
[…] 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 […]
Exploring hepatic hormone actions using a compilation of gene expression profiles
[…] 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 […]
A combined approach exploring gene function based on Worm Human Orthology
[…] 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 […]
Identification of functional SNPs in the 5 prime flanking sequences of human genes
[…] 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 […]
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