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Volume 2, Issue 1      January-March, 2014

IN SILICO ANALYSIS OF SMAD4 INVOLVED IN HEPATOCELLULAR CARCINOMA
 

Muhammad Asif Rasheed*, Sara Afzal, Fatima Tariq, Shazia Mannan
COMSATS Institute of Information Technology, Sahiwal

ABSTRACT
Hepatocellular carcinoma (HCCa, also called malignant hepatoma) is a primary malignancy of the liver. Most cases of HCCa are secondary to either a viral hepatitide infection (hepatitis B or C) or cirrhosis (alcoholism) being the most common cause of hepatic cirrhosis. HCCa is the fifth most common cancer and the third most common cause of cancer death worldwide. Many different proteins are involved in HCCa including insulin growth factor (IGF) II , signal transducers and activators of transcription (STAT) 3, STAT4, mothers against decapentaplegic homolog 4 (SMAD 4), fragile histidine triad (FHIT), SIRT etc. The present study includes the bioinformatics analysis of SMAD 4 protein in order to understand the proteomic aspect and improvement of the diagnosis of the disease. Different information related to proteins were gathered from different databases e.g. official Symbol and chromosome location were taken from National Center for Biotechnology Information (NCBI) Gene database. Structural weight (mass of the protein) was taken from Uniprot database. Length of amino acids chain was taken from NCBI Protein database. Different domains of protein were taken from InterProScan. The proteins details related to diseases were checked from Online Mendelian Inheritance in Man (OMIM) database. The multiple sequence alignments of top eight closest sequences to these proteins were performed by Claustalw2. Structure of the protein and evaluation of the quality of the structures were included from Easy modeller and Pymol programs. This analysis not only helped to gather the information related to the protein at one place but also analyzed the structure and quality of the protein. Moreover, the present study also included the phylogenetic analysis among different species based on the protein.  Keywords: Hepatocellular carcinoma, NCBI, Uniprot, InterProScan, OMIM, Pymol

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