A Relational Database for the Caenorhabditis elegans Nematode

1. A Relational Database for the Caenorhabditis elegans Nematode By Andrea Adams Advisors: Dr. Ed Harcourt and Dr. Lorraine Olendzenski Bioinformatics is a field in which computer systems are used to process experimental data from biological experiments. Working with members of the Biology Department, I have constructed a relational database system to aid in processing the data from gene expression experiments done using a microarray or DNA chip. The Anoxia Gene Expression Group is specifically interested in genes expressed in neurons and mitochondria in the nematode C. elegans when it is raised in an environment devoid of oxygen. To identify these genes easily from among over 22,500 candidates, I mined data from the existing SAGE and Mitores databases to construct two relational databases: one detailing all of the genes expressed in neurons, and the other detailing the genes expressed in mitochondria. Once experimental data has been loaded into the database, the biologists use a web interface to access and query the databases. These queries involve selecting experimental data for genes expressed in neurons, mitochondria, or both that are either up-regulated or down-regulated around a cutoff value specified by the user. Anoxia (gene name) expression log2 transformation Spot Report 1 - Cab_rep1 31.79220779 4.990601302 C25A1.8 0.674094708 -0.568976797 F21F3.6 0.630179028 -0.666166351 F25H2.9 42 5.392317423 F56H1.4 1.052631579 0.074000581 H06O01.1 0.909822534 -0.136342928 T20F10.2 0.752657005 -0.409935534 T23H2.5 0.887591241 -0.172032664 Y65B4BR.6 0.441941075 -1.178074072 Y71F9B.8 1.722222222 0.784271309 C16A11.1 14 3.807354922 C30B5.6 1.163793103 0.218834602 F33A8.2 1.016260163 0.023269779 F37H8.5 0.794369645 -0.3321176 R07G3.1 999 9.964340868 T01E8.4 2.264150943 1.178970141 Y48E1B.10 1.776859504 0.829329612 Y54G9A.7 0.741444867 -0.431588676 C16A3.4 0.7775 -0.36308542 C28H8.12 0.831417625 -0.266354764 F40H6.1 0.752427184 -0.410376122 F48E8.3 1.068027211 0.094948404 R07E5.14 0.902465166 -0.148056848 R74.3 0.871660555 -0.198161669 Y41C4A.13 0.798319328 -0.324962155 Y48A6B.3 0.959970888 -0.05893744 Microarry is analyzed using Magic Tool Gene data from the C.elegans in a microarray chip C.elegans Genes are prepared and put into the microarray Output from the Microarray Experiment ID CELE3HIDHAC CELE02381;DE Probable 3-hydroxyisobutyrate dehydrogenase, mitochondrial (HIBADH).OS Caenorhabditis elegans.OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae;OC Caenorhabditis.CH CHROMOSOME:V; 20491975..20495334; strand +.LO Mitochondrial (By similarity).DR UNIPROT; Q9XTI0DR ENSEMBL; B0250.5DR ENSEMBL; B0250.5DR EMBL; AL031630DR EMBL; Z81453XX//ID CELEACADM_1AC CELE02384;DE Probable acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor (MCAD).OS Caenorhabditis elegans.OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae;OC Caenorhabditis.CH CHROMOSOME:X; 17214839..17213071; strand -.LO Mitochondrial matrix (By similarity).DR UNIPROT; Q22347DR ENSEMBL; T08G2.3DR ENSEMBL; T08G2.3.1DR EMBL; U42838DR Pfam; PF00441DR Pfam; PF02770DR Pfam; PF02771FH Key Location/Qualifiers FHFT sig_peptide UNIPROT::Q22347:1..15FT /note="Mitochondrion (By similarity)"XX//ID CELEACADM_2AC CELE02385;DE Probable acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor (MCAD).OS Caenorhabditis elegans.OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae;OC Caenorhabditis.CH CHROMOSOME:X; 17214839..17213090; strand -.LO Mitochondrial matrix (By similarity).DR UNIPROT; Q22347DR ENSEMBL; T08G2.3DR ENSEMBL; T08G2.3.2DR EMBL; U42838DR Pfam; PF00441DR Pfam; PF02770DR Pfam; PF02771FH Key Location/Qualifiers FHFT sig_peptide UNIPROT::Q22347:1..15FT /note="Mitochondrion (By similarity)"XX//ID CELEACONAC CELE00020;DE Probable aconitate hydratase, mitochondrial precursor (Citrate hydro-lyase) (Aconitase).OS Caenorhabditis elegans.OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae;OC Caenorhabditi Mitores Data for C.elegans http://biology.plosjournals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pbio.0030030&id=20204 http://www.research.vt.edu/resmag/resmag2001/article_photos/microarray.GIF Experiment, Sage data, and Mitores data are parsed and inserted into MySQL Final Output Database Query System Sample Experiment Gene A vs B log Description C05C10.3 -0.839085 CoA-transferase). C05C10.3 -0.839085 CoA-transferase). C05C10.3 -0.839085 CoA-transferase). T09F3.2 -0.819846 Hypothetical protein T09F3.2 (Carrier protein) (C2). T09F3.2 -0.819846 Hypothetical protein T09F3.2 (Carrier protein) (C2). C34E10.6 -0.69623ATP synthase beta chain C34E10.6 -0.69623ATP synthase beta chain C34E10.6 -0.69623ATP synthase beta chain C34E10.6 -0.69623ATP synthase beta chain C05D11.12 -0.672993 flavoprotein dehydrogenase) (Lethal protein 721). Experiment is queried to retrieve genes expressed in Mitochondria, Neurons, or both that are above or below a given cutoff value. atcgctgactgtggaca 1583 coding_RNA 1 + Y75B12B.5 cyn-3 "Peptidyl-prolyl cis-trans isomerases" ccacatcgaggtcatct 1401 coding_RNA 1 + Y48G8AL.8a rpl-17 "C. elegans RPL-17 protein, contains similarity to Pfam domain PF00237 (Ribosomal protein L22p/L17e)" ccacatcgaggtcatct 1401 coding_RNA 1 + Y48G8AL.8b rpl-17 "C. elegans RPL-17 protein, contains similarity to Pfam domain PF00237 (Ribosomal protein L22p/L17e)" gtcaacgaagctgagaa 1201 coding_RNA 1 + F26D10.3 hsp-1 "HSP-1 heat shock 70kd protein A" tcttgtgtggtggtttg 683 SAGE Data for C.elegans