Specialized DBMSs

Front-end Tools - DBGET

Front-end Tools - Entrez
 Standardized
Vocabularies/Ontologies
<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE go:go> <go:go xmlns>
<go:version timestamp="Wed May 9 23:55:02 2001" /> <rdf:RDF> <go:term
rdf:about="http://www.geneontology.org/go#GO:0003673"> <go:accession>GO:0003673</go:accession>
<go:name>Gene_Ontology</go:name> <go:definition></go:definition> </go:term> <go:term
rdf:about="http://www.geneontology.org/go#GO:0003674"> <go:accession>GO:0003674</go:accession>
<go:name>molecular_function</go:name> <go:definition>The action characteristic of a gene product.</go:definition>
<go:part-of rdf:resource="http://www.geneontology.org/go#GO:0003673" /> <go:dbxref>
<go:database_symbol>go</go:database_symbol> <go:reference>curators</go:reference> </go:dbxref>
</go:term> <go:term rdf:about="http://www.geneontology.org/go#GO:0016209"> <go:accession>GO:0016209</go:accession>
<go:name>antioxidant</go:name> <go:definition></go:definition> <go:isa
rdf:resource="http://www.geneontology.org/go#GO:0003674" /> <go:association> <go:evidence evidence_code="ISS">
<go:dbxref> <go:database_symbol>fb</go:database_symbol> <go:reference>fbrf0105495</go:reference>
</go:dbxref> </go:evidence> <go:gene_product> <go:name>CG7217</go:name>
<go:dbxref> <go:database_symbol>fb</go:database_symbol> <go:reference>FBgn0038570</go:reference> </go:dbxref>
</go:gene_product> </go:association> <go:association> <go:evidence evidence_code="ISS"> <go:dbxref>
<go:database_symbol>fb</go:database_symbol> <go:reference>fbrf0105495</go:reference> </go:dbxref> </go:evidence>
<go:gene_product> <go:name>Jafrac1</go:name> <go:dbxref> <go:database_symbol>fb</go:database_symbol>
<go:reference>FBgn0040309</go:reference> </go:dbxref> </go:gene_product> </go:association> </go:term> </rdf:RDF>
%lt;/go:go>
Part III – Collaboration with Emory
• Figure
from
Darnell, nucleus
mRNA
Lodish,
and
Baltimore
,
Molecula DNA
r Cell
Biology,
2nd ed,
Scientific
American cell membrane
Books,
Inc., New rough ER and
York, mitochondrion cytosol ribosomes
1990
 Human Mitochondrial Map
MITOMAP: http://www.gen.emory.edu/mitomap
F T
DEAF 1555 D-Loop
V 12s
rRNA Cyt b LHON 14484
0 P

LDYS 14459
16s E ND6
rRNA
America A
MELAS 3243
L

ND5
LHON 3460 ND1 America C
Africa L
I Q
L
ADPD M
H
S
4336 America D
ND2
ND4
AN
Europe H Asia F
C
W Y LHON 11778
America B, ND4L

Asia B ND3
R
COI S COIII G
ATPase6
COII

D
K

MERRF 8344 ATPase8 NARP 8993/Leigh’s 8993

 MITOMAP Data
Interactions
Functional
Data

Gene-gene
Interactions mtDNA Sequence Population
Data Data Data

population
Disease
database
Data
Mitomap
 ASN.1
gene_locus ::= {
"MTTAS",
16157,
16172,
"TAS",
"termination sequence",
"[Doda, 1981 #111]"
}
 Mitomaster
“The Cuisinart of Mitochondrial DNA”

Mitochondrial DNA
Mitomaster Processed Data
Sequences
 Data Processing
• Alignments
• SNP Detection
• Haplogroup Identification
• Phylogenetic Analysis
• Disease Diagnostics
 What’s a SNP?

50 kb DNA

• “Single Nucleotide Polymorphism”

• Frequency = 1,000 bp
• Used in Genome Mapping & Analysis
Alignments
Trees
Haplogroups
ANTHROPOLOGICAL STUDIES

Human Mitochondrial DNA Migrations

9,500

73,000 15,000 17,000

51,000
34,000
re c e nt

130,000

Se que nc e Dive rg e nc e Ra te = 2.2% / MYR

Open Source Bioinformatics
Software

• www.bioinformatics.org
• www.bioperl.com
• alignment
• viewers
• database
• objects
CMM Informatics System

Web Page
Database Server
User
(ORACLE)
Interface

Revised Mitomap DB

Sequencing Data

Processed Data
Microarrays
Microarray Results
 Microarray Datamining
User inputs a
list of genes and
their expression Gene thesaurus
profiles
title
Extract keywords Functional
Local MEDLINE
from annotation keyword abstract
in our Oracle
fields in GenBank, selection
MESH database
SwissProt algorithm

User selects
background list, Calculate
other parameters Keyword - gene
background word
clustering algorithm
lists, stop list
Microarray data
Output: ordered
ArrayStat list of keywords with
associated genes
SOM, SOTA

Output: expression patterns

Temporal patterns
of genes with same keyword(s)
of gene expression