Table 1 |
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MatchMiner LookUp search options |
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| Identifier type |
Input algorithm |
Output algorithm |
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| Name (Gene symbol, alias or descriptive name) |
HUGO then Alias |
HUGO then Alias |
| Starts with Official. If not found, proceeds through all other sources. |
Returns the HUGO name. If no name is flagged as HUGO, returns all aliases. |
|
| ALL (HUGO and Alias) |
ALL (HUGO and Alias) |
|
| Searches all data sources for all matches to the symbol and flags those that are HUGO. |
Returns all gene symbols and flags the HUGO symbol. |
|
| Official |
Official |
|
| Searches all data sources for match as the HUGO name. |
Returns the HUGO name. If not found, nothing is returned. |
|
| Long |
Long |
|
| Searches all data sources for descriptive name. |
Returns all descriptive names. |
|
| GenBank accession number |
ALL |
ALL |
| Searches all data sources starting with UCSC known genes, then LocusLink, UniGene
and UCSC ESTs until match found. |
Returns accession number from UCSC known genes. If not found, proceeds through UniGene
then UCSC EST. |
|
| Data-source specific |
Data-source specific |
|
| Look up input in a specific data source. |
Returns accession numbers found in a particular data source. |
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| IMAGE clone |
UniGene |
UniGene |
| Only data source with IMAGE clone ids. |
Returns all IMAGE clone IDs associated with the UniGene |
|
| Cytogenetic location |
ALL |
ALL |
| Searches all gene indexes for matching chromosome band. |
Returns chromosome band from UCSC sequence to band translation. If not found, proceeds
through all other sources with multiple bands listed separately. |
|
| UCSC |
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| Returns chromosome band from UCSC sequence to band translation. |
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| Database id |
UniGene |
UniGene |
| Searches gene index for matching UniGene id. |
Returns UniGene id. |
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| Affymetrix |
Affymetrix |
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| Searches gene index for matching Affymetrix probe set identifier. |
Returns Affymetrix probe set identifier. |
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| Sequence location number (bp) |
Not implemented |
Transcription Start |
| Returns transcription start from UCSC Known Genes. If not found, proceeds to UCSC
EST. |
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| FISH clone |
UCSC |
UCSC |
| Searches UCSC FISH clones for match to gene index based on sequence position overlap
with UCSC known genes. |
Returns FISH clone id. |
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Bussey et al. Genome Biology 2003 4:R27 doi:10.1186/gb-2003-4-4-r27 |
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