Exam 1 Review Flashcards
What is bioinformatics?
use computer DATABASES/algorithms to analyze proteins/genes/complete collection of DNA (genome) comprises an organism.
What is medical informatics?
intersection between healthcare and data acquisition/analysis, bringing together the skills of healthcare + computer sciences to improve healthcare/patient outcomes
What distinguishes bioinformatics from other informatics disciplines?
distinguished by its particular focus on DNA & proteins
Genomics
study of genomes of organisms
What 6 specialized subtypes genomics?
Cognitive genomics, neurogenomics, funtional genomics, metagenomics, epigenomics, pharmacogenomics
Cognitive genomics =
changes cognitive processes associated with genetic profiles
Neurogenomics =
genetic influences on development and function nervous system
Functional Genomics =
describes gene and protein functions and interactions
often uses transcriptomics
Metagenomics =
study of metagenomes (ex. - genetic material recovered directly environmental samples)
Epigenomics =
study of reversible modifications on cell’s DNA/histones that affect gene expression w/o altering DNA sequence
Pharmacogenomics =
study role of genome in drug metabolism & response
All informatics disciplines are concerned with
systematizing and analyzing increasingly large datasets
Type/level of data and ex. - of their specific databases –> expression variation
Study expression variation @ mRNA data level.
Specific databases = dbEST, UniGene, GEO profiles, GEO datasets
dbEST
Division of GenBank
-contains sequence data and other information on “single-pass” cDNA sequences from numerous organisms
UniGene
system automatically divides GenBank sequences into NON-redundant set gene-oriented clusters
- -transcriptome database
- -provides: protein similarities, gene expression, cDNA clones, genomic location
GEO Profiles
store gene expression profiles from GEO dataset
–profiles = presented as charts display expression level of one gene across all samples w/in dataset
GEO Datasets
store original submitter-supplied records (series, samples, platforms) as well as curated datasets
–curated datasets = cleaned, organized, and filtered of irrelevant data/info
3 different perspectives/levels of life which bioinformatics can be applied
cell, individual, all life on earth (all 3 main domains life)
Bioinformatics @ cell level =
study molecular sequence to provide insight into broad range of biological problems
Bioinformatics @ individual (organism) =
cell –> organism = individuals whole genome (collection of genes) + genes expressed as RNA transcripts + protein products
- *Individual Organism, bioinformatics describe CHANGES:
- –through developmental time
- –across body regions
- –variety physiological/pathological states
Bioinformatics tools applied to all 3 major branches life –> collection & analysis molecular seq for all species =
= variation between or w/in species allows for deduction of EVOLUTIONARY HISTORY life
Why are globins useful example to illustrate bioinformatics discipline?
Good ex.- role gene/whole-genome duplication in promoting EVOLUTIONARY INNOVATION (fxnal diversification)
–vertebrate key globin protein evolution (oxidative metabolism & O2 signal pathways) traced back to origin = 2 whole-genome duplication events origin
Web-based Graphical User Interface
graphical representation = user interacts software via graphical icons
--includes: Central resources (NCBI, EBI, DDBJ), genome browsers (NCBI, UCSC, Ensembl), GUI software (Partek), &
Command lines
CONSOLE/TEXT-BASED representations = user types commands to interact/operate software or devices
–includes = programming languages + command-line software
