DermaMeth : Human DNA Methylation database for genes associated with dermatological disorders

Search Result

The result page mainly contains five different sections, the first section is regarding the Methylation Data that provides details regarding Gene Name, Disease Name, Disease Class and Disease ID, Gene ID, Chromosome No., p-value, Transcript, Methylation Type, Gene Expression, PubMed ID, Methylation percentage, Methylation probe, % of GC Content and Karyotype. The next section is SNiP and mutation data that gives information regarding the Gene Name, Gene ID, dbSNP, Swiss-Prot-AC, Amino Acid –change. The third section is Ontology Data that gives information related to Biological Process, Molecular Function, Cellular Component and KEGG Pathway. The fourth section provides the General Gene related information that provides information such as OMIM ID, UniProt ID, Accession Numbers, Gene name, HGNC ID, PDB ID, Vega gene ID, Gene Start (bp), Gene End (bp), RefseqID, Entrez Gene ID, Chromosome, Enzyme IDs, Synonyms, Gene Family ID, Ensembl Gene ID, PubMed IDs and UCSC ID. The last section is regarding the Interaction Data that gives information regarding the interaction between Gene-Disease, Gene-Pathway, Gene-Molecular Function, Gene-Methylation Type, Gene-Gene Expression, Disease-Pathway, Disease-Molecular Function, Disease-Methylation Type and Disease-Gene Expression.

Methylation Data

• Disease ID - Medical Subject Headings (MeSH) is a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences; it serves as a thesaurus that facilitates searching. Created and updated by the United States National Library of Medicine (NLM) Description - It provides the description of the gene queried.

• p-value - p-value is the probability of obtaining a test statistic result between tumor and normal sample groups.

• Transcript - It gives the RefSeq: NCBI Reference Sequence Database which is a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

• Methylation Type - It provides the type methylation for each gene queried and there are more than 15 type methylation categories.

• Gene Expression - It provides the associations between gene methylation and gene expression for the gene queried.

• Methylation percentage - It provides the methylation percentage of each gene queried.

• Methylation probe - Illumina Methylation Assay is used for methylation probes on the Illumina 27k methylation array.

• % of GC Content - GC-content is the percentage of nitrogenous bases on a DNA or RNA molecule that are either guanine or cytosine

SNiP and mutation data

• dbSNP - A SNP is a variation that occurs at a specific position in a single nucleotide within the genome. (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the NCBI in collaboration with the National Human Genome Research Institute (NHGRI)

• Amino Acid –change - Amino acid substitution affects protein function

• Ontology Data - The Ontology defines concepts/classes used to describe gene function, and relationships between these concepts.

• Biological Process - It is series of events accomplished by one or more ordered assemblies of molecular functions.

• Molecular Function - It relates to the activity that can be performed by individual gene products, but some activities are performed by assembled complexes of gene products.

• Cellular Component - Cellular Component refers to the unique, highly organised substance of which cells, and thus living organisms, are composed.

• KEGG Pathway - It provides the molecular interaction and reaction networks for Metabolism, Genetic Information Processing, Environmental Information Processing, Cellular, Organismal Systems and Human Diseases.

General Gene related information

• OMIM ID - OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine.

• UniProt ID - It provide information about the biological function of proteins derived from the research literature.

• Vega gene ID - It is a repository for high-quality gene models produced by the manual annotation of vertebrate genomes.

• Gene Family ID - A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions.

• Ensembl Gene ID - It is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.

Interaction Data

• Gene-Disease - It gives the interaction between the disease and respective genes.

• Gene-Pathway - It gives the interaction between the pathway and respective genes.

• Gene-Molecular Function - It gives the interaction between the Molecular function and respective genes.

• Gene-Methylation Type - It gives the interaction between the methylation type and respective genes.

• Gene-Gene Expression - It gives the interaction between the expression and respective genes.

• Disease-Pathway - It gives the interaction between the pathway and respective diseases.

• Disease-Molecular Function - It gives the interaction between the Molecular function and respective diseases.

• Disease-Methylation Type - It gives the interaction between the methylation type and respective diseases.

• Disease-Gene Expression - It gives the interaction between the expression and respective diseases.