A Relational Database for the Caenorhabditis elegans Nematode

Anoxia (gene name) expression log2 transformationSpot Report 1 - Cab_rep1 31.79220779 4.990601302C25A1.8 0.674094708 -0.568976797F21F3.6 0.630179028 -0.666166351F25H2.9 42 5.392317423F56H1.4 1.052631579 0.074000581H06O01.1 0.909822534 -0.136342928T20F10.2 0.752657005 -0.409935534T23H2.5 0.887591241 -0.172032664Y65B4BR.6 0.441941075 -1.178074072Y71F9B.8 1.722222222 0.784271309C16A11.1 14 3.807354922C30B5.6 1.163793103 0.218834602F33A8.2 1.016260163 0.023269779F37H8.5 0.794369645 -0.3321176R07G3.1 999 9.964340868T01E8.4 2.264150943 1.178970141Y48E1B.10 1.776859504 0.829329612Y54G9A.7 0.741444867 -0.431588676C16A3.4 0.7775 -0.36308542C28H8.12 0.831417625 -0.266354764F40H6.1 0.752427184 -0.410376122F48E8.3 1.068027211 0.094948404R07E5.14 0.902465166 -0.148056848R74.3 0.871660555 -0.198161669Y41C4A.13 0.798319328 -0.324962155Y48A6B.3 0.959970888 -0.05893744

atcgctgactgtggaca 1583coding_RNA1+Y75B12B.5cyn-3"Peptidyl-prolyl cis-

trans isomerases"ccacatcgaggtcatct 1401

coding_RNA1+Y48G8AL.8arpl-17"C. elegans RPL-17

protein, contains similarity to Pfam domain PF00237 (Ribosomal protein L22p/L17e)"ccacatcgaggtcatct 1401

coding_RNA1+Y48G8AL.8brpl-17"C. elegans RPL-17

protein, contains similarity to Pfam domain PF00237 (Ribosomal protein L22p/L17e)"gtcaacgaagctgagaa 1201

coding_RNA1+F26D10.3hsp-1"HSP-1 heat shock

70kd protein A"tcttgtgtggtggtttg 683

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

Sample Experiment Gene A vs B log DescriptionC05C10.3 -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 chainC34E10.6 -0.69623ATP synthase beta chainC34E10.6 -0.69623ATP synthase beta chainC34E10.6 -0.69623ATP synthase beta chainC05D11.12 -0.672993 flavoprotein dehydrogenase) (Lethal protein 721).

C.elegansGene data from the C.elegans in

a microarray chip

Output from the Microarray Experiment

Mitores Data for C.elegans

SAGE Data for C.elegans

Database Query System

Final Output

Genes are prepared and put

into the microarray

Microarry is analyzed using

Magic Tool

Experiment, Sage data, and Mitores data are

parsed and inserted into

MySQL

Experiment is queried to retrieve genes expressed in

Mitochondria, Neurons, or both that are above or below a

given cutoff value.

By Andrea AdamsAdvisors: Dr. Ed Harcourt and Dr. Lorraine Olendzenski

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

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.