Download Caenorhabditis elegans

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.
Gene data from the C.elegans in
a microarray chip
C.elegans
Genes are
prepared and put
into the microarray
http://biology.plosjournals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pbio.0030030&id=2
0204
721).
Sample Experiment
A vs B log
-0.839085
Description
CoA-
-0.839085
CoA-
-0.839085
CoA-
-0.819846
Hypothetical
(Carrier protein)
-0.819846
Hypothetical
(Carrier protein)
-0.69623ATP
synthase beta
-0.69623ATP
synthase beta
-0.69623ATP
synthase beta
-0.69623ATP
synthase beta
-0.672993
flavoprotein
dehydrogenase)
(Lethal protein
Anoxia (gene name)
expression
log2 transformation
Spot Report 1 - Cab_rep1
C25A1.8
F21F3.6
F25H2.9
F56H1.4
H06O01.1
T20F10.2
T23H2.5
Y65B4BR.6
Y71F9B.8
C16A11.1
C30B5.6
F33A8.2
F37H8.5
R07G3.1
T01E8.4
Y48E1B.10
Y54G9A.7
C16A3.4
C28H8.12
F40H6.1
F48E8.3
R07E5.14
R74.3
Y41C4A.13
Y48A6B.3
31.79220779
0.674094708
0.630179028
42
1.052631579
0.909822534
0.752657005
0.887591241
0.441941075
1.722222222
14
1.163793103
1.016260163
0.794369645
999
2.264150943
1.776859504
0.741444867
0.7775
0.831417625
0.752427184
1.068027211
0.902465166
0.871660555
0.798319328
0.959970888
4.990601302
-0.568976797
-0.666166351
5.392317423
0.074000581
-0.136342928
-0.409935534
-0.172032664
-1.178074072
0.784271309
3.807354922
0.218834602
0.023269779
-0.3321176
9.964340868
1.178970141
0.829329612
-0.431588676
-0.36308542
-0.266354764
-0.410376122
0.094948404
-0.148056848
-0.198161669
-0.324962155
-0.05893744
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
http://www.research.vt.edu/resmag/resmag2001/article_photos/microarray.GIF
Final Output
Gene
C05C10.3
transferase).
C05C10.3
transferase).
C05C10.3
transferase).
T09F3.2
protein
T09F3.2
(C2).
T09F3.2
protein
T09F3.2
(C2).
C34E10.6
chain
C34E10.6
chain
C34E10.6
chain
C34E10.6
chain
C05D11.12
Microarry is
analyzed using
Magic Tool
Experiment is queried to
retrieve genes expressed in
Mitochondria, Neurons, or
both that are above or below a
given cutoff value.
Database Query System
Experiment,
Sage data, and
Mitores data are
parsed and
inserted into
MySQL
atcgctgactgtggaca
Output from the
Microarray Experiment
Mitores Data for
C.elegans
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