Cours Bioinformatique 2008-2009: TP2 Researchers have identified a gene that is involved in breast cancer. Your task in this exercise is to use bioinformatics tools and databases to find useful information about this gene. The protein sequence is: 1) Identification of this sequence and its function >Seq1 MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAY EFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPF LQPHGQQVPYYLENEPSGYTVREAGPPAFYRPNSDNRRQGGRERLASTNDKGSMAMESAK ETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQAC RLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDGEGRGEVGSAGDMRAANLWPSPLMIKR SKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINW AKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEG MVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLD KITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLL LEMLDAHRLHAPTSRGGASVEETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV Use blast to find which gene is it. Have a look in pubmed to see how many articles are retrieved with the name of this gene. It s obvious that you cannot read all these articles to understand the function of this gene. You need distilled information from public databases. What is the SWISSPROT entry name? What is the function of this gene? ESR1_HUMAN It s an estrogen receptor: FUNCTION: Nuclear hormone receptor. The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. In what diseases is it known to be involved? Have a look at wikipedia first and then in OMIM database in the NCBI web site.
In what tissues and diseases is the gene expressed? Tissues: Adrenal gland, layrynx, mmary gland, ovary, pituitary gland, prostate, muscle. Diseases: uterine tumor, ovarian tumor, adrenal tumor, breast (mammary gland) tumor, pancreatic cancer, chondrosarcoma normal, lung tumor. Look for information at the expression profile in Unigene database of NCBI. What is the unigene identifier? Hs.208124 2) Analysis of a mutant Researchers have identified a mutation of this gene in various tumors. What is the nature of this mutation? Go to the ENSEMBL web site and compare your sequence with the longest transcript. Tip: Use blast to compare the mutant with the normal sequence. Look at the exon structure of the normal and diseased transcript. Is this finding confirmed by literature? Look at the section Gene function of this gene in OMIM. >Mutant MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAAN AQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLENEPSG YTVREAGPPAFYRPNSDNRRQGGRERLASTNDKGSMAMESAKETRYCAVCNDYASGYHYGVWSCEGCKA FFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGGHNDYMCPATNQCTIDKNRRKS CQACRLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDGEGRGEVGSAGDMRAANLWPSPLMIKRSKKNS LALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHD
QVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGE EFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILS HIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPTSRGGASVEETDQSHLATAGSTSSHSLQK YYITGEAEGFPATV Use blast to compare the mutant with the normal sequence. You can also use Dotlet for the comparison normal sequence versus mutant (and also mutant vs mutant): http://myhits.isb-sib.ch/cgi-bin/dotlet (the documentation is available here: http://myhits.isbsib.ch/util/dotlet/doc/dotlet_help.html) In the first picture (nomral sequence vs mutant), there is a break in the line, indicated a segement duplicated. In the second picture (Mutant vs Mutant), the duplicated fragment is more visible.
Extract the extra sequence and blast it again. You will see that its the zinc finger of estrogen receptor alpha. It s a duplication. Go to Ensembl and search using ESR1 for human
The third exon was duplicated You go to OMIM and find similar things in literature on the section GENE FUNCTION, third paragraph. 3) Protein Interaction High expression of the above gene is not enough for development of breast cancer. Another gene (AIB1) has to be highly expressed as well. * Do the two genes physically interact? Yes, they are interacting. Use the HPRD database (Human Protein Reference Database) to find this out. Use the relevant links to literature to understand the nature of this association between the two genes. * What are its synonyms? One of the alternative names (synonyms) of AIB1 is NCOA3
* What is the link between this and the previous gene? click invivo: in vitro and you can read the paper in which the interaction was described.