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 31.7922077
9 4.990601302 C25A1.8 0.674094708 -0.568976797 F21
F3.6 0.630179028 -0.666166351 F25H2.9 42 5.3923174
23 F56H1.4 1.052631579 0.074000581 H06O01.1 0.9098
22534 -0.136342928 T20F10.2 0.752657005 -0.4099355
34 T23H2.5 0.887591241 -0.172032664 Y65B4BR.6 0.44
1941075 -1.178074072 Y71F9B.8 1.722222222 0.784271
309 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 T01
E8.4 2.264150943 1.178970141 Y48E1B.10 1.776859504
0.829329612 Y54G9A.7 0.741444867 -0.431588676 C16
A3.4 0.7775 -0.36308542 C28H8.12 0.831417625 -0.26
6354764 F40H6.1 0.752427184 -0.410376122 F48E8.3 1
.068027211 0.094948404 R07E5.14 0.902465166 -0.148
056848 R74.3 0.871660555 -0.198161669 Y41C4A.13 0.
798319328 -0.324962155 Y48A6B.3 0.959970888 -0.058
93744
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 CELE02381DE Probable
3-hydroxyisobutyrate dehydrogenase, mitochondrial
(HIBADH).OS Caenorhabditis elegans.OC
Eukaryota Metazoa Nematoda Chromadorea
Rhabditida Rhabditoidea Rhabditidae
PeloderinaeOC Caenorhabditis.CH
CHROMOSOMEV 20491975..20495334 strand .LO
Mitochondrial (By similarity).DR UNIPROT
Q9XTI0DR ENSEMBL B0250.5DR ENSEMBL
B0250.5DR EMBL AL031630DR EMBL Z81453XX//ID
CELEACADM_1AC CELE02384DE Probable
acyl-CoA dehydrogenase, medium-chain specific,
mitochondrial precursor (MCAD).OS
Caenorhabditis elegans.OC Eukaryota Metazoa
Nematoda Chromadorea Rhabditida Rhabditoidea
Rhabditidae PeloderinaeOC Caenorhabditis.CH
CHROMOSOMEX 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
UNIPROTQ223471..15FT
/note"Mitochondrion (By similarity)"XX//ID
CELEACADM_2AC CELE02385DE Probable acyl-CoA
dehydrogenase, medium-chain specific,
mitochondrial precursor (MCAD).OS
Caenorhabditis elegans.OC Eukaryota Metazoa
Nematoda Chromadorea Rhabditida Rhabditoidea
Rhabditidae PeloderinaeOC Caenorhabditis.CH
CHROMOSOMEX 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
UNIPROTQ223471..15FT
/note"Mitochondrion (By similarity)"XX//ID
CELEACONAC CELE00020DE Probable aconitate
hydratase, mitochondrial precursor (Citrate
hydro-lyase) (Aconitase).OS Caenorhabditis
elegans.OC Eukaryota Metazoa Nematoda
Chromadorea Rhabditida Rhabditoidea
Rhabditidae PeloderinaeOC Caenorhabditi
Mitores Data for C.elegans
http//biology.plosjournals.org/perlserv/?request
slideshowtypefiguredoi10.1371/journal.pbio.003
0030id20204
http//www.research.vt.edu/resmag/resmag2001/artic
le_photos/microarray.GIF
Final Output
Experiment, Sage data, and Mitores data are
parsed and inserted into MySQL
Database Query System
Sample
Experiment Gene A vs B
log
Description C05C10.3 -0.839085
CoA-transferase). C0
5C10.3 -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 cy
n-3 "Peptidyl-prolyl cis-trans isomerases" ccacatc
gaggtcatct 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 1
201 coding_RNA 1 F26D10.3 hsp-1 "HSP-1 heat
shock 70kd protein A" tcttgtgtggtggtttg 683
SAGE Data for C.elegans