Exam 1 Review

Question 1

What is bioinformatics?

Answer 1

use computer DATABASES/algorithms to analyze proteins/genes/complete collection of DNA (genome) comprises an organism.

Question 2

What is medical informatics?

Answer 2

intersection between healthcare and data acquisition/analysis, bringing together the skills of healthcare + computer sciences to improve healthcare/patient outcomes

Question 3

What distinguishes bioinformatics from other informatics disciplines?

Answer 3

distinguished by its particular focus on DNA & proteins

Question 4

Genomics

Answer 4

study of genomes of organisms

Question 5

What 6 specialized subtypes genomics?

Answer 5

Cognitive genomics, neurogenomics, funtional genomics, metagenomics, epigenomics, pharmacogenomics

Question 6

Cognitive genomics =

Answer 6

changes cognitive processes associated with genetic profiles

Question 7

Neurogenomics =

Answer 7

genetic influences on development and function nervous system

Question 8

Functional Genomics =

Answer 8

describes gene and protein functions and interactions

often uses transcriptomics

Question 9

Metagenomics =

Answer 9

study of metagenomes (ex. - genetic material recovered directly environmental samples)

Question 10

Epigenomics =

Answer 10

study of reversible modifications on cell’s DNA/histones that affect gene expression w/o altering DNA sequence

Question 11

Pharmacogenomics =

Answer 11

study role of genome in drug metabolism & response

Question 12

All informatics disciplines are concerned with

Answer 12

systematizing and analyzing increasingly large datasets

Question 13

Type/level of data and ex. - of their specific databases –> expression variation

Answer 13

Study expression variation @ mRNA data level.

Specific databases = dbEST, UniGene, GEO profiles, GEO datasets

Question 14

dbEST

Answer 14

Division of GenBank

-contains sequence data and other information on “single-pass” cDNA sequences from numerous organisms

Question 15

UniGene

Answer 15

system automatically divides GenBank sequences into NON-redundant set gene-oriented clusters

• -transcriptome database
• -provides: protein similarities, gene expression, cDNA clones, genomic location

Question 16

GEO Profiles

Answer 16

store gene expression profiles from GEO dataset

–profiles = presented as charts display expression level of one gene across all samples w/in dataset

Question 17

GEO Datasets

Answer 17

store original submitter-supplied records (series, samples, platforms) as well as curated datasets

–curated datasets = cleaned, organized, and filtered of irrelevant data/info

Question 18

3 different perspectives/levels of life which bioinformatics can be applied

Answer 18

cell, individual, all life on earth (all 3 main domains life)

Question 19

Bioinformatics @ cell level =

Answer 19

study molecular sequence to provide insight into broad range of biological problems

Question 20

Bioinformatics @ individual (organism) =

Answer 20

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

Question 21

Bioinformatics tools applied to all 3 major branches life –> collection & analysis molecular seq for all species =

Answer 21

= variation between or w/in species allows for deduction of EVOLUTIONARY HISTORY life

Question 22

Why are globins useful example to illustrate bioinformatics discipline?

Answer 22

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

Question 23

Web-based Graphical User Interface

Answer 23

graphical representation = user interacts software via graphical icons

--includes: 
Central resources (NCBI, EBI, DDBJ), 
genome browsers (NCBI, UCSC, Ensembl), 
GUI software (Partek), &

Question 24

Command lines

Answer 24

CONSOLE/TEXT-BASED representations = user types commands to interact/operate software or devices

–includes = programming languages + command-line software