A Relational Database for the Caenorhabditis elegans Nematode Anoxia (gene name)expression log2...
-
Upload
gervais-alexander -
Category
Documents
-
view
217 -
download
4
Transcript of A Relational Database for the Caenorhabditis elegans Nematode Anoxia (gene name)expression log2...
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.