An introduction to the expression data available in flymine

Summary of the expression data in FlyMine

BDGP: in-situ hybridisation FlyFish: RNA_seq: from the modENCODE project. High-throughput data. Raw data analysed by FlyBase. FlyAtlas tissue-specific expression Developmental time-course

The diverse nature of the expression datasets in FlyMine means that is difficult to search them together and compare the results.

in-situ hybridisation data

FlyMine contains two sources of in-situ hybridisation data - BDGP and FlyFish. Both sources provide gene expression data during fly development. Although the time points used vary sightly between the datasets it is possible to compare the data produced by these two sources. This is because each stage range is mapped to the FlyBase embryonic development CV. So, for example, if BDGP measure expression at stage range 7-8 and FlyFish at 8-9, searching for genes expressed at embryonic stage 8 will return results for both of these. Two template searches provide data from both these sources. The first allows you to specify the genes you are interested in, the second shows data for all genes but at a specified developmental stage:

1. Gene --> FlyFish + BDGP insitu data

2. [Stage --> FlyFish + BDGP insitu data] (http://www.flymine.org/release-37.0/template.do?name=Stage_FlyFishBDGP&scope=all)

A number of other template searches allow you to search each of these datasets independently - navigate to the templates tab and filter on expression, or enter the keywords 'BDGP' or 'FlyFish'.

Note that both BDGP and FlyFish annotate the expression patterns to the ImaGO ontology. It is possible to search the datasets using an expression term:

1. Search BDGP with an expression term

2. Search FlyFish with an expression term.

Developmental gene expression

FlyMine contains two further sources of developmental gene expression data - the first from a 2002 microarray study, Arbeitman et al, which reports gene expression patterns for nearly one-third of all Drosophila genes during a complete time course of development and the second, more recent RNA_seq data from the modENCODE project. Again, the diverse nature of these two studies makes it difficult to directly compare the data in a single search. Several templates are available for each source individually.

### The Arbeitman dataset:

This is a microarray dataset and the expression level is given as the median signal ratio. The reference set was pooled mRNA from all stages. Therefore, to identify if a gene is expressed at a particular stage you need to look at or filter on this value (e.g show only genes expressed with a median signal ratio greater then 2.0). For example, the following template allows you to look at the expression of a particular gene or list of genes and optionally filter on the median signal ratio and the developmental stage. Of course these filters can be further changed or removed from within your results table:

Gene --> Microarray time course expression data from Arbeitman et al

Also note that this dataset can be searched either on general developmental stages, eg embryo, or more specific stages, eg embryo 11-12 hours. Separate template searches are available for each:

1. General stage

2. Specific stage

   The RNA_seq dataset:

This dataset was generated by labs from the modENCODE project. However, the raw data was analysed by FlyBase. For full details on the analysis process see: FlyBase RNA_seq analysis. This dataset provides expression levels across developmental stages as well as some adult tissue expression levels. The expression levels have been binned into the following categories:

1. Extremely low expression: 1-10;
2. Very low expression: 11-100;
3. Low expression: 101-400;
4. Moderate expression: 401-1400;
5. Moderately high expression: 1401-4000;
6. High expression: 4001-10000;
7. Very high expression: 10001-100000;
8. Extremely high expression: 100001-2000000;

A number of templates allow this data to be searched. Navigate to the templates tab and filter on expression and enter the keyword RNA_seq.

Expression in adult fly tissues

FlyMine contains data from the FlyAtlas project. This data is affymetrix array data giving the expression levels of genes in adult fly tissues. It gives you a quick answer to the question: where is my gene of interest expressed/enriched in the adult fly? The following tissues have been studied:

Adult carcass Adult eye Adult fat body Adult heart Brain Crop Head Hindgut Larvae hindgut Larval CNS Larval carcass Larval fat body Larval midgut Larval salivary gland Larval trachea Larval tubule Male accessory glands Mated spermatheca Midgut Ovary S2 cells Salivary gland Testis Thoracicoabdominal ganglion Tubule Virgin spermatheca Whole Fly

For each gene & tissue, you're given the mRNA signal (how abundant the mRNA is), the mRNA enrichment (compared to whole flies), and the Affymetrix present CALL (out of 4 arrays, how many times it was detectably expressed). A number of template searches allow you to explore this data. Navigate to the templates tab and enter the keyword FlyAtlas. The templates include various options for filtering on the mRNA signal, mRNA enrichment and affymetrix call.