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Flashcards in Lecture 25 Deck (27):
1

What is defined as an interdisciplinary field that develops methods for understanding complex biological data? It combines computer science, stats, math, and engineering to study and process biological data.

Bioinformatics

2

What is defined as the study, invention, and implementation of structures and algorithms to improve communication, understanding, and management of medical information?

Biomedical informatics

3

Common uses of bioinformatics include:

A. Understanding organizational patterns within nucleic acids and protein seq
B. ID candidate genes
C. ID SNPs
D. Sequencing DNA
E. All of the above
F. A, B, and C

E. All of the above

4

Matching:

1. Searchable, integrated database of human genes that provides comprehensive, updated, and user-friendly info on all known and predicted human genes
2. International organization of scientists involved in human genetics. Warehouse of info.
3. Full of data of previously performed studies that no one was interested in so went unanalyzed

A. HUGO - Human genome organization
B. GEO - Gene expression omnibus
C. GeneCards

1. C.
2. A.
3. B.

5

What contains annotations and links for 2500 bioinformatic databases and software tools?

Online Bioinformatics Resources Collection

6

Children's Mercy Genome Center provides:

A. In-hospital gene sequence analysis that allows for time sensitive medical decision making
B. Relays samples to company who can sequence DNA
C. Has ability to sequence DNA but methods do not allow for timely decision making
D. All of the above

A. In-hospital gene sequence analysis that allows for time sensitive medical decision making

7

CMH Genome Center algorithm mechanism:

A. Compare patients clinical presentation to worldwide medical databases to ID candidate genes and analyze patient's DNA focusing on candidate genes
B. Ability to identify genes critical for understanding a clinical presentation in a timely fashion
C. Not useful for making timely decisions in NICU
D. All of the above
E. A and B

E. A and B

8

T/F: CMH algorithm improves the reliability of genetic testing but not the speed.

False, CMH algorithm improves both the speed and reliability of genetic testing.

9

What is the advantage of next ge sequencing for newborn screening?

A. One test for all conditions
B. One test for one condition
C. Many tests for many conditions
D. All of the above

C. Many tests for many conditions

10

Which type of analysis is a comprehensive studies of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data?

A. HUGO
B. GEO
C. Ingenuity
D. Partek

D. Partek

11

Which of the following is a web-based software application that enables you to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP micro arrays; metabolomics, proteomics, and RNA seq experiments? Allows you to put 1 paper in and the software matches it with papers that have similar topics.

A. Ingenuity
B. GeneCards
C. HUGO
D. Bioinformatics

A. Ingenuity

12

T/F: Partek aligns the reads to standardized human genome reference sequence

True

13

What is the most important aspect of Partek?

Menu-driven (make selections from menus)

14

Which of the following are advantages of Partek?

A. Menu-driven
B. Creates work flow
C. Group genes into functional categories (systems assessment)
D. Can assess accumulated sequence variation on candidate pathways
E. Can assess post-transcriptional processing
F. A, B and C
G. All of the above

G. All of the above

15

Which of the following are aspects of Ingenuity?

A. Assessment of multiple levels of integration with easy access to primary data that supports relationships
B. Uploads expression data into ingenuity pathways
C. Evaluates known pathways for nonrandom gene enrichment (over expression of genes that may implicate disease)
D. Output may not be worth price
E. A, B, and C
F. All of the above

E. A, B, and C

16

What at is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship?

OMIM - Online Mendelian Inheritance in Man

17

T/F: OMIM useful for NKX2.5 analysis bc it is associated with multiple phenotypes

True

18

Why may OMIM be useful in analysis of inheritance patterns of Tetralogy of Fallot?

Multiple genes associated with TOF

OMIM has info on all genes and how these genes affect phenotype of TOF

19

The Cancer Genome Atlas (TCGA):

A. Will Identify genomic chances in various types of cancer
B. Will Help us understand what turns normal cells into cancer cells
C. Cannot detect specific signatures
D. Identified certain areas of genome commonly affects in certain types of cancer
E. A, B, and C
F. A, B, and D

F. A, B, and D

20

What is worlds largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer?

COSMIC - Catalog of somatic mutations in cancer

21

What is a tool that contains the reference sequence and working draft assemblies for a large collection of genomes?

Type in known gene and vast amount of genome sequence data on gene will pop up

UCSC Genome browser

22

Which project is in place to ID/map all functional elements and regulatory feature in the human genome sequence?

ENCODE project - ENCyclopedia Of DNA Elements

23

Deep map of human regulatory DNA

1. What is it
2. What method/project creates this

1. Map of all changes in regulatory DNA from time of fertilized egg to elderly
2. ENCODE

24

What is a public functional genomics database of array and sequence-based expression profiles?

GEO

25

Importance of GEO in Bittel's lab's hypothesis that Splicing is under-studied and may play large role along with gene expression in biliary atresia.

- Used GEO to re-analyzed data for scaRNA and splicing variation
- Proved that scaRNA levels change as zebrafish develop
- Proved that splicing isoforms exist
- Consistnet with hypothesis BUT doesn't prove it
- Opened door for funding for future projects

26

Most important point about Bittel's lab and GEO

Did not have to perform ANY experiments to prove findings and publish a paper

27

What is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins and may have an association with disease phenotypes

Gene set enrichment (aka functional enrichment analysis)