BioMart: a research data management tool for the biomedical sciences

Transcription

1 Yale University From the SelectedWorks of Rolando Garcia-Milian 2014 BioMart: a research data management tool for the biomedical sciences Rolando Garcia-Milian, Yale University Available at:

2 BioMart: a research data management tool for the biomedical sciences Rolando Garcia- Milian Biomedical Sciences Research Support Rolando.milian@ufl.edu

3 Contents Introduction... 3 Examples of Queries... 5 Q.1 How to retrieve the Ensembl mouse genes and genomic locations in the first 10 Mbp of chromosome 1 region (Smedley et al. 2009)... 5 Q.2 Retrieving 1 kb of upstream sequences from a cluster of human genes identified by an expression profile experiment on an Affymetrix Genechip U95Av2 (Smedley et al. 2009)... 9 Q. 3 The following list of SNPs resulted from a 2014 GWAS study- obtain: variation name, source, chromosome number and position, SIFT prediction, HGNC symbol, and MIM morbid description Q. 4 Find the pathogenic SNPs reported for the retinoblastoma RB1 (Ensembl ID: ENSG ), variation source, location, and the MIM morbid description Q. 5 Using BioMart Central Portal for gene set enrichment analysis References

4 Introduction BioMart ( is a freely available open source system that allows performing complex queries across different databases- through a single web interface - located in distant geographical areas. It was originally developed for the Ensembl genome browser. BioMart has been integrated into widely used software such as Galaxy, BioConductor, Cytoskape, etc. Its interface is also used by data portals such as Ensembl, Wormbase, Gramene, Reactome, etc. (see Fig. 2) BioMart provides a solution: generic software that researchers can use on top of any data source. All BioMart websites have similar look and feel (see Fig 1) Things you can do with BioMart: export gene data, sequences, and other databases ID Figure 1- Similar look and feel of BioMart integrated into different databases and portals. In this example: WormMart, Ensembl BioMart, and Reactome BioMart 3

5 Figure 2- BioMart has been integrated into different databases and portals (Smedley et al. 2009) Figure 3- Data available at the Ensembl Biomart (Kinsella et al. 2011) 4

6 Examples of Queries Q.1 How to retrieve the Ensembl mouse genes and genomic locations in the first 10 Mbp of chromosome 1 region (Smedley et al. 2009) Go to the Ensembl genome browser main page - Click on the BioMart link located on the menu bar. Choose the Ensembl Genes 73 from the CHOOSE DATABASE dropdown menu and the Mus musculus genes (GRCm38p.1) as your dataset from the CHOOSE DATASET dropdown menu. 5

7 Click on Filters bar located in the left hand pane. Expand the REGION section - in the main right hand pane- by clicking on the plus sign. Set the Chromosome to 1, the Gene Start and Gene End filters to 1, and 10,000,000 (coincides with default values in this example) respectively. 6

8 Click on Count to find out how many results would be returned. In this example: 58 results will be returned. Select the data fields you would like to view or download by clicking on the Attributes link located in the left hand pane. Expand the GENE section located in the right hand pane. Select 7

9 Ensembl Gene ID, Associated Gene name, Chromosome Name, GeneStart (bp), and Gene End (bp). Click on the Results button located on top of the right hand pane. In order to view your 58 results in the same page, click on the View dropdown menu and set it to 100 rows. The format can also be changed and exported as hypertext markup language (HTML), Excel (XLS), FASTA, tab-separated values (TSV), comma-separated values (CSV), or gene structure format (GFF). 8

10 The notification to option is useful when the number of results is too big and cause timeout issues. The user will receive an containing a link when the results are generated and stored on the server-side. The Unique results only option is useful for removing redundant rows in the output Q.2 Retrieving 1 kb of upstream sequences from a cluster of human genes identified by an expression profile experiment on an Affymetrix Genechip U95Av2 (Smedley et al. 2009) Begin by clicking on the New button. This will open a new query session. Select Ensemble Genes 73 or the most current one from the CHOOSE DATABASE dropdown menu and Homo sapiens genes (GRCh37.p12) 9

11 Click on Filters bar located in the left hand pane. Expand the GENE section - in the main right hand pane- by clicking on the plus sign. Set the ID is limit[max 500 advised to Affy hg u95av2 probeset ID(s) - allows the user to upload a file of experimentally relevant Affymetrix probeset IDs from this Genechip. Enter IDs by cutting and pasting into the text box (see example ID list below) 10

12 Copy-paste the following Affy IDs 31527_at 40380_at 32767_at 560_s_at 31610_at 35412_at 1391_s_at 1667_s_at 39236_s_at 34769_at 36104_at 40807_at 966_at 967_g_at 34775_at 33255_at 41213_at 33165_at 37667_at 31583_at 36837_at 39772_at 32497_s_at 34177_at 36167_at 41380_at 36204_at 11

13 Select the data fields you would like to view or download by clicking on the Attributes link located in the left hand pane. Click on Sequences button located in the right hand pane. Expand the SEQUENCES section, select Flank (Gene) as your region. Check the Upstream flank and enter 1000 as the number of bases. Expand the Header Information to see the variety of attributes that can be selected for the FASTA header line of the sequence file. Check the Ensembl Gene ID, Associated Gene Name, Chromosome Name, Gene Star (bp), Gene End (bp) 12

14 You may click on Count to find out how many results would be returned. In this example: 40 results will be returned. Click on the Results button located on top of the right hand pane. You should get a FASTA view record with the Attributes already selected. 13

15 Q. 3 The following list of SNPs resulted from a 2014 GWAS study- obtain: variation name, source, chromosome number and position, SIFT prediction, HGNC symbol, and MIM morbid description. Cook et al. (2014) A genome-wide association study of prostate cancer in West African men. Hum Genet May;133(5): doi: /s z. Epub rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs

16 Go to Ensembl BioMart Select Ensembl Variation 75 from the drop-down menu under CHOOSE DATABASE. Choose Homo Sapiens Short Variations (SNPand indels (GRC37.p13) from the drop-down menu under CHOSE DATASET. Clik on Filters on the right hand pane and then click on the plus sign next to GENERAL VARIATION FILTERS 15

17 Check the box Filter by Variation Name (e.g. rs123, CM00001), and copy and paste you SNPs list into the box next to this filter. Click on Attributes and make sure to check Variation name, Variation source, Chromosome name, Position on Chromosome. In order to get the official gene symbol, we will have to cross the Ensembl Variation data with the Ensembl Genes data. Click on the Dataset link to at the bottom of the left bar and select the Ensembl Genes 75 Homo sapiens genes from the drop-down menu under CHOOSE ADDITIONAL DATASET Click on Attributes under that Dataset and make sure to check the HGNC symbol and MIM Morbid Description boxes. 16

18 Click on the Results button and then check Unique results only. Select All: to view the results as HTML in a new tab. 17

19 Q. 4 Find the pathogenic SNPs reported for the retinoblastoma RB1 (Ensembl ID: ENSG ), variation source, location, and the MIM morbid description From Ensembl BioMart, select Ensembb Variation 75 Choose Homo Sapiens Short Variations (SNPand indels (GRC37.p13) from the drop-down menu under CHOSE DATASET. 18

20 Click on the Filter Link and then on the plus sign next to the GENE ASSOCIATED FILTERS. Check the Ensembl Gene ID(s) box and enter the Ensembl gene ID for the RB1 gene ENSG in the box. Expand the GENERAL VARIATION FILTERS: by clicking on the plus sign next to this section. Scroll down and check the box for Clinical significance and select pathogenic from the list of categories inside the box. 19

21 Click on the Dataset at the bottom of the left column and select Ensemble Genes 75 Homo sapiens as the dataset from the dropdown menu. Click on the Atributes link under the second Dataset link, expand the EXTERNAL section by clicking on the plus signal next to it. Check the MIM Morbid Description box. Click on the Results button and then check Unique results only. Select All: to view the results as HTML in a new tab. You can uncheck the Ensembl Gene and Transcript IDs if you do not want them to appear in your results. 20

22 Q. 5 Using BioMart Central Portal for gene set enrichment analysis List of down-regulated genes obtained after analyzing the GEO Dataset GSE ,25 dihydroxyvitamin D effect on prostate epithelial cell line RWPE1: time course -Affymetrix Human Genome U133 Plus 2.0 Array _at _at _at _s_at _at _at _at _at _at _at _at _s_at _a_at _at _at _a_at _at _at _at _s_at _at _at _s_at _at _at _s_at _at _at _at _at _at _at _at _at _at _at _at _s_at _s_at _at _at _a_at _at _s_at _at _at _at _at _at _s_at _at _s_at _at _at _at _at _s_at _at _at _at _a_at _s_at _x_at _at _at _at _s_at _x_at _at 21

23 _at _s_at 38037_at _s_at _s_at _s_at _at _s_at _s_at _x_at _s_at _at _at _at _x_at _s_at _at _x_at _at _x_at _at _s_at _at _at _s_at _at _at _at _at _s_at _at _at _x_at _at _at _at _s_at _at _s_at _at _s_at _s_at _at _s_at _s_at _s_at _s_at _at _a_at _at _at _at _at _s_at _at _at _s_at _s_at _at _at _s_at _at _a_at _at _at _s_at _at _s_at _at _at _s_at _s_at _s_at _s_at _x_at _s_at _at _s_at _at _at _at _x_at _s_at _at _at _a_at _s_at _at _at _at _s_at _s_at _s_at _s_at _at _at _at _at _s_at _at _at _at _at _a_at _s_at _at _x_at _a_at _a_at _at _at _at _at _at _a_at _at _s_at _s_at _s_at _s_at _at _at _at _at _s_at _x_at _at _s_at _at _at _at _at _at _a_at _at _at _s_at _at _at _s_at _at _at _at _at _s_at _at _at _s_at _s_at _s_at _at _s_at _at _at _s_at _s_at _s_at _at _a_at

24 203390_s_at _at _at _at _at _at _at 35666_at _at _at _s_at _at _at _at _at _x_at _s_at _s_at _x_at _at _s_at _at _s_at _at _s_at _at _at _at _at _s_at _s_at _at Open the BioMart Central Portal Click on the TOOLS link located in the left column. Click on the enrichment analysis link. Copy and paste the list of the above Affymetrix identifiers inside the Gene list box. Select Affy hgu 133 plus 2 probeset IDs from the drop-down menu. 23

25 Click on the plus sign next to FILTERS- you can change the Cut off (P-value). Click on the plus sign next to ANNOTATIONS and check the Reactome and MIM boxes. Finally, click on the SUBMIT button to see the results. 24

26 A new window will open showing the progress of your work. Once the analysis is finished, results will be shown on a new window. Click on the respective network buttons for Gene Ontology (GO), Reactome, and MIM 25

27 References Baker M (2012) Quantitative data: learning to share. Nature Methods 9: Retrieved from Kasprzyk A (2013) BioMart: driving a paradigm change in biological data management Database bar049 doi: /database/bar049 - Retrieved from Kinsella RJ, Kahari A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King G, Staines D, Derwent P, Kerhornou A, Kersey P and Paul Flicek (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database Database (Oxford) Jul 23; 2011:bar030. doi: /database/bar030 - Retrieved from Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G and Arek Kasprzyk (2009) BioMart biological queries made easy. BMC Genomics 10: 22. Retrieved from Video Tutorials on Biomart UVA on Biomart BioMart an Introduction Variation IDs to HGNC symbols with BioMart How to convert gene IDs Gene orthologs via Biomart 26