HELPFUL QUESTIONS
updated October 7, 2004
How do I find it? Chose the questions related to your starting point. Under each starting point are listed a number of questions that address common FlyBase searches. The discussion of each question includes detailed steps to help you find your answer, as well as a link to TRY IT. Clicking on TRY IT will open a new window with the appropriate FlyBase page already loaded. You can then undertake your own search while following the instructions. If you prefer not to open a second window, read the instructions and then use the navigation bar at the top of this page to reach the appropriate FlyBase query page.
WHAT ARE YOU STARTING WITH?
WHAT WOULD YOU LIKE TO KNOW?
I think the gene name that I have is outdated. How do I find out current information about this gene?
Use the Genes query form. TRY IT. Enter the outdated gene symbol and choose symbol/synonym/name. FlyBase maintains all old gene names and symbols as synonyms, so this search should bring up the gene report under the current name. To check for all previous names of your gene (but not all previous FlyBase ID numbers), click on the link for synonyms from the gene report, or look for these two entries in the full gene report: Synonyms and Secondary ID (to get all previous or secondary FlyBase ID numbers).
How can I determine if my gene has had other names in the past?
Use the Genes query form. TRY IT. Enter the gene symbol and choose symbol or symbol/synonym/name. To check for all previous names of your gene, click on the link for synonyms from the synopsis gene report, or look for these two entries in the full gene report: Synonyms and Secondary ID (to get all previous or secondary FlyBase ID numbers).
How many different alleles of this gene have been studied?
Use the Allele query form. TRY IT. Enter the name of your gene in the box and choose either full name ( i.e. yellow) or Gene symbol or name( i.e. y). Then click on "Submit." You should be given a hit list of all the alleles of your gene that are in FlyBase. Click on any entry to be taken to an allele report. If you would like to download this list, see below .
Use the Genes query form. TRY IT. Enter the name of your gene in the box and choose symbol, symbol/synonym/name or Gene/allele full name and click "Submit." If there is more than one match to your query, you will be given a hit list from which to chose the appropriate gene report. From this hit list, click on the number entered in the "alleles" column to go directly to the allele sub-report for your gene. If there is a single match to the gene query, you will go directly to a gene report. From there, chose the link to alleles to obtain a list of all alleles of the gene known to FlyBase.
Are there any alleles of this gene generated by EMS (or any other specific mutagen)?
Use the Genes query form. TRY IT. Enter the name of your gene in the box and choose symbol, symbol/synonym/name or Gene/allele full name, and then move down the page to "Extended query options for mutant alleles." There you will find a listing of mutagens. Select the mutagen you are interested in (EMS is listed as ethyl methanesulfonate) and click Submit. You will be given a list of alleles generated by that type of mutagenesis. If there is only one allele, you will be taken directly to an allele report.
Use the Alleles query form. TRY IT. Enter the gene symbol and select gene symbol or name. Then go to the box labeled "Mutagen" and find ethyl methanesulfonate (or any other mutagen) and submit. You will be given a hit list of alleles of your gene that are the result of the selected mutagen.
Are there any gain of function alleles (or any other allele class) of my gene?
Use the Genes query form. TRY IT. Enter the name of your gene in the box and choose symbol, symbol/synonym/name or Gene/allele full name, and then move down the page to "Extended query options for mutant alleles." There you will find a listing of allele classes. Chose gain of function from the menu, and submit. This search will generate a list of all alleles of your gene classified as gain of function alleles. If there is only one, you will be given an allele report.
Use the Alleles query form. TRY IT. Enter the gene symbol and select gene symbol or name. Then go to the box labeled "Class" and select gain of function and submit. This search will generate a list of all gain of function alleles of your gene. If there is only one, you will be given an allele report.
Are any mutant alleles of my gene available from public stock centers?
Use the Genes query form. TRY IT. Enter the name of your gene and choose either symbol/synonym/name or Gene/allele full name and click Submit. If you are taken to a hit list of genes, look under the column labeled "stocks." If there is a value listed, this is the number of stocks available. Clicking on the number will take you to a stock hit list, and links for ordering the stocks are available there. If you are taken directly to a gene report, then click on the listing for stocks under "subsections" and you will go to the same list of available stocks.
Use the Stocks query form. TRY IT. Enter the symbol for your gene and submit. You will be given a hit list of stocks which contain alleles of your gene.
Is a specific mutant allele of my gene available from a stock center?
Use the Allele query form. TRY IT. If you know the exact name of the allele, enter it and chose symbol/synonym/name. If you are only sure of the gene name, enter that and chose gene name. If you are taken to an allele hit list, look for the column labeled Stocks. If there is a value entered next to the allele of your choice, click on it to be taken to a stock list, and you can order the stock from there. If you are taken directly to an allele report, the available stocks will be listed, with a link to the stock report.
Use the Stocks query form. TRY IT. Enter the symbol of the allele you are interested in and submit. Remember to enclose superscripts in square brackets [ ]. If there are stocks with this specific allele, you will be given a hit list of those stocks. If there is a single hit, you will be given a stock report directly.
Are there any chromosomal aberrations at or near my gene?
Use CytoSearch. TRY IT. CytoSearch allows you to search by cytological location or by the symbol or ID number of your gene of interest. Chose gene symbol (or synonym) from the first menu and enter your gene symbol in the first box. To obtain the aberrations at or near your gene, remove the check marks from all boxes except those aberrations of interest. You will be given a list of aberrations known to be in the region of your gene. The aberration names will be linked to aberration reports. If there are stocks available at Bloomington, there will be a link to a stock report as well. You may also chose to show only those features which have available stocks.
Use the Aberrations query form. TRY IT. To find aberrations that are in the region of your gene, enter the cytological location of the gene and click on submit. You will be given a hit list of aberrations that are found in that region. To find aberrations that are alleles of your gene, enter the gene symbol followed by [* (i.e., y[* ), select symbol/synonym and submit.
For balancer chromosomes, use the Balancers query. TRY IT. Enter the chromosome you are interested in and submit. The resulting hit list has links to the aberration reports and to stock reports if they are available.
I would like to see what the chromosomal region near my gene looks like. How do I find a micrograph of this region?
Use GBrowse. TRY IT. Enter the name of your gene and click GO. You will be given a map of the region around your gene, with your gene labeled in red. Below the map you will find micrographs of polytene chromosomes hybridized to a BAC that includes your gene.
For images of all of the chromosomes, use the link from the Anatomy and Images page to find the polytene chromosome electron micrographs of Saura, Saura and Sorsa. TRY IT .
Where is my gene known to be expressed?
Use the Gene query form. TRY IT. Enter the name of your gene and select symbol or symbol/synonym/name and submit. When you get the gene report, look for the subsection "EXPRESSION AND PHENOTYPES." There you will find listed the known expression patterns for the gene as well as a summary of allele phenotypes, a listing of phenotypic classes and descriptions of mutant phenotypes. Not all of this information will be available for all genes. In addition, look at the listing of External Database links under the heading Gene Ontology. There may be links there to sites external to FlyBase that will show expression patterns.
Go to the Anatomy and Images page for links to external sources of expression pattern images. TRY IT. A large collection of expression pattern images may be found at FlyView, Flytrap (Edinburgh) and FlyTrap (Yale).
Has the phenotype of a specific allele of my gene been described?
Use the Allele query form. TRY IT. If you know the exact name of the allele, enter it and choose symbol/synonym/name. If you are only sure of the gene name, enter that and chose gene name. Then submit. If you are taken to an allele hit list, select the allele you are interested in to go to the allele report. In the allele report, there may be a subheading entitled "expression and phenotypes" which will list data available for this allele. If there is no such listing, look for the headings "phenotypic class" and "mutant phenotype" for information about this allele's phenotypes.
Are there any reporter constructs for my gene?
Use the Transgene Constructs query form. TRY IT. Use the reporter construct menu located on the right side of the page. Scroll through this to look for your gene, select the construct of interest, and submit.
Use the Genes query form. TRY IT. Enter the name of your gene and select symbol/synonym/name and submit. From the gene report, look for the sub report called Constructs and Insertions. This will list all constructs and insertions associated with your gene. Look for the listing of reporter constructs in this sub report. There will be links to the individual constructs and information about the presence or absence of expression data.
How do I find all published references to my gene?
Use the References query form. TRY IT. Enter the symbol or ID number of your gene and submit. You will be give a list of all references that include your gene. If you would like to download this list, see below .
Use the Genes query form. TRY IT. Enter the name of your gene and select symbol/synonym/name and submit. If there is more than one hit for your entry, look at the column of the hit list labeled "References." Click on the value entered for your gene and you will be taken to the list of references. If there is only one match to your entry, look for the subsection called References in the gene report.
How do I find an annotation for this gene?
Use the Basic Annotation query form. TRY IT. If you know the CG number for the gene, enter it and select symbol, then submit. If you do not know the CG number, enter the symbol for your gene, select synonym, and submit. You may not get a match if you select symbol, as annotations are often listed by their CG number only. If there is more than one match to your query, you will be taken to a hit list from which you can select the annotation of your choice.
How do I find the gene, transcript and protein sequences for this gene?
Use the Basic Annotation query form. TRY IT. If you know the CG number for the gene, enter it and select symbol, then submit. If you do not know the CG number, enter the symbol for your gene, select synonym, and submit. You may not get a match if you select symbol, as annotations are often listed by their CG number only. If there is more than one match to your query, you will be taken to a hit list from which you can select the annotation report that you are interested in. From the annotation report there are links to DNA and amino acid sequences as well as BLAST results.
Use the Genes query form. TRY IT. Enter the gene symbol and select symbol/synonym/name and submit. You will either go to a hit list of possible matched or directly to a gene report. From the gene report, you can chose to view the gene region, transcript or translation of your gene. Under the subheading "Similar genes and sequences" you will find links to sequence accession numbers for your gene as well as for those of similar genes from other species.
How do I find clones of this gene and how can I order them?
Use the Basic Annotation query form. TRY IT. If you know the CG number for the gene, enter it, select symbol, then submit. If you do not know the CG number, enter the symbol for your gene, select synonym, and submit. You may not get a match if you select symbol, as annotations are often listed by their CG number only. If there is more than one match to your query, you will be taken to a hit list from which you can select the annotation report that you are interested in. In the annotation report you will see a list of cDNAs and ESTs. Clicking on each ID number will give you the sequence of each. Many clones are available from the Drosophila Genomics Resource Center (DGRC). For a listing of other sources of clones and similar resources, see the FlyBase Clones page or the FlyBase Drosophila Resources page.
Are there similar sequences in Drosophila?
Use the Basic Annotation query form. TRY IT. If you know the CG number for the gene, enter it, select symbol, then submit. If you do not know the CG number, enter the symbol for your gene, select synonym, and submit. You may not get a match if you select symbol, as often annotations are listed by their CG number only. From the annotation report, scroll down the page to the blastx_dros heading. Each BLAST hit has a link to the sequence of the similar fly genes. Or, from the annotation report, next to the heading sequence, get the sequence of your gene in FASTA format. Copy the sequence, then go to the Fly BLAST page. TRY IT. Enter the sequences and search. This will return all similar Drosophila sequences.
Use the Genes query form. TRY IT. Enter the gene symbol and select symbol or symbol/synonym/name and submit. You will either go to a hit list of possible matched or directly to a gene report. From the gene report, chose the sub report "similar genes and sequences" where you will find links to DNA, RNA and protein sequences.
I would like to see what the chromosomal region near my gene looks like. How do I find a micrograph of this region?
Use GBrowse. TRY IT. Enter the name of your gene and click GO. You will be given a map of the region around your gene, with your gene labeled in red. Below the map you will find micrographs of polytene chromosomes hybridized with a BAC that includes your gene.
Use the Gene query form. TRY IT. Enter the name of your gene and select symbol/synonym/name and click submit. If you are taken to a hit list of possible genes, choose the gene you are interested in to go to the gene report. From the gene report, click on the Gene Region Map link under the small map of the gene. You will be taken to a GBrowse map of this gene region. Your gene of interest will be labeled in red. Below the map you will find micrographs of polytene chromosomes hybridized with a BAC that includes your gene.
Use the Basic Annotation query form. TRY IT. If you know the CG number for the gene, enter it and select symbol, then submit. If you do not know the CG number, enter the symbol for your gene, select synonym, and submit. You may not get a match if you select symbol, as annotations are often listed by their CG number only. If there is more than one match to your query, you will be taken to a hit list from which you can select the annotation of your choice. From the annotation report page, click on the link to Gene Region Map (GBrowse), located under the small map of the gene.You will be taken to a GBrowse map of this gene region. Your gene of interest will be labeled in red. Below the map you will find micrographs of polytene chromosomes hybridized with a BAC that includes your gene.
Has the protein(s) encoded by my gene been characterized?
Use the Polypeptide query form. TRY IT. Enter the name of your gene, select associated gene, and submit. If there is more than one match to your query, you will be given a hit list from which to select a polypeptide report. The polypeptide report contains information on expression and biochemical characterization of the protein as well as a list of references.
Use the Genes query form. TRY IT. Enter the gene symbol and select symbol/synonym/name and submit. You will either go to a hit list of possible matched or directly to a gene report. From the gene report, select the link to the sub report "Proteins and Transcripts." This will list all polypeptides with links to each individual report.
Has the transcript(s) encoded by my gene been characterized?
Use the Transcript query form. TRY IT. Enter the name of your gene, select associated gene, and submit. If there is more than one match to your query, you will be given a hit list from which to select a transcript report. In the transcript report you will find information about expression patterns and characterization of the transcript. A list of references to this transcript can be found as well.
Use the Genes query form. TRY IT. Enter the gene symbol and select symbol/synonym/name and submit. You will either go to a hit list of possible matched or directly to a gene report. From the gene report, select the link to the sub-report "Proteins and Transcripts." This will list all transcripts, with links to each individual report.
How do I find all of the genetic elements in a chromosomal region?
Use CytoSearch. TRY IT. Chose "cytolocation" from the menu and enter the map region of interest in the box. Alternatively, you can chose "sequence region" from the menu and enter sequence coordinates. You may specify which features to retrieve by checking or unchecking the features boxes.
Use the Genes query form TRY IT. Under "extended query options", enter the cytologic map range you are interested in and submit. You will be given a hit list of all genes known to be in that region. If you are interested in other genetic elements, go to the bottom of the genes query form to "result data class" and chose retrieve related insertions or aberrations instead.
Use the Aberrations query form. TRY IT. Enter the values for the cytological range and enter. At least one end of the chromosomal aberration will be in your region of interest.Use the Insertion query form. TRY IT. Enter the values for the minimum and maximum cytological locations and submit. At least one end of the insertion will be in your region of interest.
Use GBrowse. TRY IT. Enter the coordinates of the region that you are interested in (1 Mb or smaller) in the box labeled "Gene ID or region" and click GO. You may change the genetic elements that appear on the map using the Display Settings menu found at the bottom of the page.
How do I find a balancer marked with lacZ (or another marker)?
Use the Balancer query form. TRY IT. Select the chromosome that you are interested in and select lacZ (blue balancers) or one of the other markers. You will be given a list of balancer chromosomes. If there is a number entered in the column labeled "stocks," then there are stocks available from the public stock centers. Clicking on that number will link you to stock reports.
Where do I find micrographs of this region of a polytene chromosome?
Use GBrowse. TRY IT. If you know the name of a gene in your region, enter that name and chose the size of the region to display. Or, you can enter the coordinates of your region directly. In order to obtain a detailed view of your region, you must specify a coordinate range less than 1,000,000 base pairs. Enter the gene name or coordinates in the box labeled "Gene ID or region" and click GO. Under the map of the region, you will be given images of in situ hybridizations of BACs to this region as well as micrographs of the chromosomes themselves.
For images of all of the chromosomes, use the link from the Anatomy and Images page to find the polytene chromosome electron micrographs of Saura, Saura and Sorsa. TRY IT .
What genes are associated with the trachea (or any other anatomical term?)
Use the Expression Pattern search form. TRY IT. Enter the anatomical term in the "find" box and submit. The resulting vocabulary report will give a definition of the term and list any sub terms. If this is the term you are interested in, go to the upper right corner and select View-Expression pattern form and click GO. From this page, select the term and/or sub term you are interested in by checking the boxes next to the term. Then, select which genetic classes you wish to retrieve (in this case "genes") and click on "List Genetic Classes." You will be given a list of genes that are expressed in or associated with the trachea.
Use the Genes search form. TRY IT. Go to the middle of the page to the Extended Query options, and click on "Select Body parts." This will open up a new window where you can enter your term (trachea) in the search box. You will be given a list of terms that match your search. Select the one you are interested in (adult trachea, for example). You will see your term listed as well as the vocabulary hierarchy of this term. Check any (all) terms you are interested in. You may also check the box "Add All Subcomponents." Then click "add checked terms;" when these are added, close this window, and submit your genes query. You will be given a hit list of genes that are expressed in the adult trachea. If you would like to download this list, see below .
Are there any images of the trachea (or any other anatomical part) in FlyBase?
Use the Anatomy and Images browser. TRY IT. This page lists general categories of images. Images of the tracheal system may be found by clicking on the "tracheal system" link under organ system. All images of the tracheal system that have been curated by FlyBase will be found here.
Use the Anatomy and Images page. TRY IT. Enter the anatomical part you are interested in (trachea) in the "term matches" box and submit. You will be given a vocabulary report for that term. If the term is specific enough there will be an image accompanying this report. If the term needs to be refined (adult trachea), click on the term and go to that vocabulary report to see an image.
What proteins are known to be expressed in the trachea (or any other anatomical term)?
Use the Polypeptides search form. TRY IT. Find the term(s) you are interested in in the menu "Body part (where expressed), select those term(s), and submit.
What transcripts are known to be expressed in the trachea (or any other anatomical term)?
Use the Transcripts search form. TRY IT. Find the term(s) that you are interested in in the menu labeled "Body part (where expressed)", select those term(s) and submit.
How do I find genes that are involved in a specific biological process, such as meiosis?
Use the Gene Ontology Search. TRY IT. The second search box allows you to specify the type of term that you are looking for. Select "biological process" from the menu and then type in your term, such as meiosis. You will be given a list of matches to your term. Select the one that you are interested in, and you will be given a list of genes involved in that process. Clicking on each gene will take you to the gene report for that gene. If you would like to download all of the gene reports for the genes in your list, copy the list, and go to the batch download page. TRY IT. Paste your list into the box and submit your query.
Use the Genes search form. TRY IT. Go down the page to the Extended query options. Click the select GO terms button. Enter your term, such as meiosis, into the search box. You will be given a list of matches to your term. Select the one you are interested in. You will then see the GO hierarchy associated with your term, and you may chose to search for genes associated ONLY with that term or with that term plus any sub terms in the hierarchy, by clicking the appropriate boxes. Click "add checked terms" and then close to close this small window and submit your query. You will be given a hit list of genes that are involved in your biological process.
Use the Basic Annotation query form. TRY IT. The middle of this page has a menu containing the GO terms that cover 77% of the annotation records. If your term is not on this list, you may enter it in the find box at the top of the page, select "Gene Ontology term" and submit. This search will result in all genes that have been annotated and which match your term.
How do I find genes that are involved in a specific molecular function such as alkaline phosphatase?
Use the Gene Ontology Search page. TRY IT. The second search box allows you to specify the type of term that you are looking for. Select molecular function from the menu and then type in your term, such alkaline phosphatase. You will be given a list of matches to your term. Select the one that you are interested in, and you will be given a list of genes. Clicking on each gene will take you to the gene report for that gene. If you would like to download all of the gene reports for the genes in your list, copy the list, and go to the batch download page. TRY IT. Paste your list into the box and submit your query.
Use the Genes search form. TRY IT. Go down the page to the extended query options. Click the select GO terms button. Enter your term, such as alkaline phosphatase, into the search box. You will be given a list of matches to your term. Select the one you are interested in. You will then see the GO hierarchy associated with your term, and you may chose to search for genes associated ONLY with that term or with that term plus any sub terms in the hierarchy, by clicking the appropriate boxes. Click "add checked terms" and then close to close this small window, and submit your query. You will be given a hit list of genes that are involved in your molecular function.
Use the Basic Annotation query form. TRY IT. The middle of this page has a menu containing the GO terms that cover 77% of the annotation records. If your term is not on this list, you may enter it in the find box at the top of the page, select "Gene Ontology term" and submit. This search will result in all genes that have been annotated and which match your term.
How do I find genes with products involved in a specific cellular component such as golgi apparatus?
Use the Gene Ontology Search page. TRY IT. The second search box allows you to specify the type of term that you are looking for. Select cellular component from the menu and then type in your term, such golgi apparatus. You will be given a list of matches to your term. Select the one that you are interested in, and you will be given a list of genes. Clicking on each gene will take you to the gene report for that gene. If you would like to download all of the gene reports for the genes in your list, copy the list, and go to the batch download page. TRY IT. Paste your list into the box and submit your query.
Use the Genes search form. TRY IT. Go down the page to the extended query options. Click the select GO terms button. Enter your term, such as dynein complex, into the search box. You will be given a list of matches to your term. Select the one you are interested in. You will then see the GO hierarchy associated with your term, and you may chose to search for genes associated ONLY with that term or with that term plus any sub terms in the hierarchy, by clicking the appropriate boxes. Click "add checked terms" and then close to close this small window, and submit your query. You will be given a hit list of genes that are involved in this cellular component.
Use the Basic Annotation query form. TRY IT. The middle of this page has a menu containing the GO terms that cover 77% of the annotation records. If your term is not on this list, you may enter it in the "find" box at the top of the page, select "Gene Ontology term" and submit. This search will result in all genes that have been annotated and which match your term.
How do I find all of the work published by this person?
Use the References query form.TRY IT. Enter the last name (only) of the individual, select author(s) and submit.
How can I contact this person?
Use the People query form. TRY IT. Enter the name of the individual, first and/or last name but with no commas, select Name, and enter. If there is more than one match to the query you will be given a hit list. People reports include mailing and email addresses, as well as phone numbers for each individual.
FlyBase search results ("hit list")
If your search generates a large number of hits or matches, you may want to further refine your query or download the FlyBase reports. The questions below begin with a link to a book marked search result for use as an example.
How do I download all of this information so that I can use my own analytical tools?
The example is a list generated from a Genes query for genes having alleles with a lethal phenotype. TRY IT. To download this list of genes, click the Batch Download box at the top right hand corner of the query results page. This will take you toward the bottom of the page to the Batch Download Option. If you want all of the gene reports, then select "all," choose the format of the download and then click on fetch items. If you want only a subset of the gene reports, or only portions of each report, see the two question below for further information.
How do I specify what information I would like to download?The example is a list generated from a Genes query for genes having alleles with a lethal phenotype. TRY IT. Click on the Batch Download box at the top right hand corner of the results page. This will take you toward the bottom of the page to the Batch Download option. Select the gene reports that you wish to download (all or items) and then click on the "select fields" link. Choose from the Select fields list those parts of the gene reports you wish to download. For example, click on FlyBase ID, full name and references. Close this box and click " fetch items."
How can I narrow my results to better fit what I was looking for in the first place?
The example is a list generated from a Genes query for genes having alleles with a lethal phenotype. TRY IT. Click on the refine query option at the top right hand corner of the results page. This will take you to the bottom of the page to the refine query option. Here you can add qualifiers to your search such as a reference or product function. Then click on "refine query" to obtain the refined hit list of genes. Additionally, you can also elect to retrieve reports related to this list of genes. At the bottom of the refine query box you will see the word "Search Genes, retrieve...only" Here you will find a menu where you can chose to retrieve, for example, all the alleles of the genes in the list, or all insertions in these genes.
I have a collection of FlyBase ID numbers, and I would like to download all of the reports corresponding to those ID's.
Use the batch download by ID function. TRY IT. Paste or enter any type of FlyBase ID numbers into the box. Choose the format you wish the reports to be downloaded in, and submit the query.
How do I find the Drosophila genes that correspond to a large number of EST's?
Use the Batch Download Reports by ID function. TRY IT. This form allows you to enter a variety of ID numbers and retrieve FlyBase gene reports. If you have DGC ID numbers, simply enter or paste your list into the box. You may also specify the format you wish the reports to be downloaded in, and you may chose to receive all information about the genes, or select the fields to report. Then, submit the query. If any of the ID numbers do not match a FlyBase report, then you will be given an error message asking you to remove those from the list. Submit your query again after removing those IDs that do not match, and you will be able to download the rest.
My query generated a large collection of FlyBase ID's. How can I download the sequence of all of these genes?
Use the Batch Download Sequences by ID function. TRY IT. Enter FlyBase FBgn or FBan ID's into the list box and identify which type of ID's you have entered in the menu on the left. Then chose what type of sequence you would like to receive and the format of the sequence, and click on Submit Query.