MiGenes Database

The MiGenes Single Search Module is designed to be intuitive to the user; it supports a variety of accession number-based as well as textbased keyword searches through a single flexible interface. Since MiGenes pops up in a new window, please close webpages when you don't need them.

You can enter a protein accession number, which is a unique identifier, so that the number will either be recognized or not. If the number is recognized, the output will include a link to a single record screen that provides a link to extensive information about the protein collated from several sources. This single record screen includes the “mitochondrial status” assigned to the protein based on GO term assignments and curator decisions.
We also provide a free-text search permitting the user to input any string of 3 or more characters into the query field. You may enter a single accession number or a gene/protein name. Search strings are not case-sensitive. If a search identifies a single unambiguous record, only one record will be returned. Typing “all” returns all records for the selected organism. You may search with partial names and use the response to limit further searches. For example, searching the human subset with the string "NADH" or "nadh" returns 48 records. If you really want information on the 75 kDa FeS protein, you could search for NDUFS1 or NP_004997 in the accession number search, which returns only one record. To constrain the search, the user must select an organism from the drop-down list. Press the "Search" button to initiate the search.

a. Accession Number Search: please type accession number in the input box pointed by the arrow shown below. Click the “Search By Accession Number” button to initiate the search.

3. NCBI UniGene ID, for example: Dm.2294, Cel.18297, Mm.22453, Hs.546236, Rn.2549

b. Free Text Search: You can type any word or text string. For example, to search “mitochondrial ribosomal protein”, you can type: “mitochondrial ribosomal protein” or “ribosomal” or “mitochondrial” in the input box pointed by the arrow shown below. The string should be 3 or more characters long. Then choose the organism you want to search using the organism drop-down menu. If you want to search only for mitochondrial proteins, you can choose “ Mito” from the mitochondrial status menu. Otherwise choose “Related” from the status menu. Click the “Free Text Search” button to initiate the search.

The following shows a search result screen obtained by searching for human mitochondrial proteins that match “ribosom”. MiGenes displays entries matching the search criteria. For each record found, the entrez gene id, the refseq accession number, the protein description and organism name will be shown. If your search string was ambiguous, the protein you are looking for may be only one of many responses. Clicking the protein description link will direct you to the detailed single protein information page. Clicking the “Download” button will download search results into an Excel file.

As shown below, there are five tabs: A. Summary, B. Reference, C. Ortholog, D. GO Annotation, E. Curator Comment and F. Sequence.

A. The summary tab is shown by default. This screen provides the Gene Name, Gene Symbol, Entrez Gene ID and the link to the NCBI Entrez Gene page for the selected record. It also shows the mitochondrial status in MiGenes and, for human records, the ID for the OMIM database Online Mendelian Inheritance in Man. The Unigene ID and the corresponding Unigene link are displayed as well as the protein description, RefSeq mRNA accession number and corresponding NCBI entrez and UniProt links. It also displays additional names that may be applied to this protein or the corresponding gene in alternative data sources. In this tab, if the protein has isoforms, multi-alignment image of isoforms will display. In a few cases, the image is not available. We are trying to make the images as complete as possible.

B. The bibliography of PubMed references that cite this record. The PubMed ID’s are active links to abstracts in PubMed.

C. Ortholog tab lists orthologs of the protein. Clicking the protein description of an orthologous protein will direct you to the detailed information page for the selected ortholog. To make this transition more obvious, the prominent organism identifier in the upper right corner will change.

D. GO Annotations for the selected entry. This can be a long list, and can contain contradictory information, since most of this is downloaded from the GO Consortium. In most cases, the most important information available here is the definitive publication used to establish that the protein is mitochondrial (PubMed ID or PMID). You can access the abstract for such an article after selecting “bibliography” from the drop-down list.

E. Curator comments, if any have been applied to this record. Most records do not have individual curator comments.

F. Sequence information tab displays sequence, molecular weight and lenght of the protein.

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