Download 2008 Spring BioDB Homework 2

2008 Spring BioDB Homework 2
This problem set is due by 2PM, April 8, 2008. You shall upload your answers to
your web site as instructed by your TA. For all questions, please make a reference
such as screen-shot to indicate the source of your answer.
Please read the following abstract before you start working on this homework.
Gelatinases (MMP-2 and -9) and their natural inhibitors as prognostic indicators
in solid cancers.
Neoplastic growth and dissemination involve increased proteolytic activity that
is able to escape the regulative elements. Matrix metalloproteinases (MMPs),
particularly gelatinases A and B (MMP-2 and -9), play a role in tumor invasion and
angiogenesis, and they participate in cancer progression in several neoplasias. The
expression of tissue inhibitors of gelatinases, TIMPs-1 and -2, has also been shown to
be associated with the clinical course in some cancers. The prognostic value of these
markers, however, seems to vary a great deal in different neoplastic diseases. In this
review, the impact of the gelatinases and their inhibitors on the clinical course in
several solid cancers is evaluated based on the growing data from recent clinical
studies. The clinical data most often explore the overexpression of mRNA or
immunoreactive protein in tumor tissue, or measure the concentration of the
circulating proteinase or its inhibitor in pretreatment or follow-up serum samples. The
growing amount of recent clinical data suggests that the impact of gelatinases on
treatment decisions should be tested in clinical trials.
- Biochimie. 2005 Mar-Apr;87(3-4):287-97. Review.
1.
Use GeneID to predict splice sites and start and stop codons in the human
MMP-2 sequence. Identify the real sites among the predictions. Do they tend
to show high scores?
Ans: Yes!
2.
Now, use geneID to predict the set of possible exons. Compare your results
with the exon predictions with the real exons identified in the Ensembl
database.
Ans:
3.
Using a promoter prediction server, predict what transcription factors may
regulate MMP-2 gene expression. Can you correlate these transcription factors
with the functions described in the abstract above? Give a short explanation.
Ans:
SRY
No, there are no any function annotation in DAVID for SRY.
4.
Design a pair of PCR primers that can use in a typical real-time quantitative
PCR analysis with SYBR green for measuring human MMP-2 gene
expression.
Teacher said : do not to answer this question.
5.
Conduct a restriction enzyme digestion analysis on the MMP-2 cDNA
sequence.
Ans:
6.
Conduct a phylogenetic analysis of MMP2s found from at least 6 different
organisms. Which specie’s MMP-2 is the most closely related one to human
MMP-2?
Ans:
>gi|13591990|ref|NM_031054.1| Rattus norvegicus matrix metallopeptidase 2 (Mmp2), mRNA
>gi|47271505|ref|NM_008610.2| Mus musculus matrix metallopeptidase 2 (Mmp2), mRNA
>gi|149699544|ref|XM_001493281.1| PREDICTED: Equus caballus matrix metalloproteinase-2 (MMP-2), mRNA
>gi|83776607|ref|NM_001037869.1| Takifugu rubripes matrix metalloproteinase-2 (mmp-2), mRNA
>gi|12584828|gb|AF267159.1| Ovis aries gelatinase A mRNA, partial cds
>gi|47523461|ref|NM_214192.1| Sus scrofa gelatinase A (MMP-2), mRNA
Sus scrofa
7.
Retrieve the protein interacting network of human MMP-2.
Ans:
8.
Retrieve any microarray expression analysis on human MMP-2 in various
cancer tissues. Give a clear explanation on how to find it. Based on your
findings, MMP-2 is highly expressed in what cancer type in human?
(CGAP) : Melanorna, Non-small Cell Lung Cancer, CNS Cancer, Renal Cancer and
Breast Cancer
1:LOX IMVI [Melanorna]
15:HOP-62[Non-small Cell Lung Cancer]
16:HOP-92[Non-small Cell Lung Cancer]
18:SNB-19[CNS Cancer]
19:SNB-75[CNS Cancer]
20:U251[CNS Cancer]
22:SF-295[CNS Cancer]
23:SF-539[CNS Cancer]
47:RXF 393[Renal Cancer]
48:786-0[Renal Cancer]
53:HS 578T[Breast Cancer]
9.
Retrieve the following article and use DAVID to redo the functional
annotation analysis on genes listed in table 3. “Identification of gene
signatures for invasive colorectal tumor cells, A.H. Wiese et al. Cancer
Detection and Prevention 31 (2007) 282-295” Can you find MMP2 in your
analysis?
Ans:
10.
Identify a possible SNP in human MMP-2 gene.
Ans:
Or