About Cell Cycle

The cell cycle is the process by which cells duplicate themselves, grow, and prepare to divide again. It is the basis for the reproduction and sustained growth of all living organisms, and its control is also important for the proper understanding of cancer, because cancer can occur when cell cycle regulation fails. In recent years the basic mechanisms underlying cell cycle control have been unravelled, and shown to be commonto living organisms from yeast to humans.

The cell division cycle underlies the growth, development and reproduction of all eukaryotes. A wealth of information derived from molecular and cell biology experiments paired with computational tools to organize and interpret this information renders a comprehensive understanding of the mammalian cell cycle control network a reachable goal of the early 21st century.

Definition : The series of events necessary for the reproduction of a cell from the time of its birth to its division into two                       daughter cells.

Phases :

The cell cycle consists of several phases (see figure). In the first phase (G1) the cell grows and becomes larger. When it has reached a certain size it enters the next phase (S), in which DNA-synthesis takes place. The cell duplicates its hereditary material (DNA-replication) and a copy of each chromosome is formed. During the next phase (G2) the cell checks that DNA-replication is completed and prepares for cell division. The chromosomes are separated (mitosis, M) and the cell divides into two daughter cells. Through this mechanism the daughter cells receive identical chromosome set ups. After division, the cells are back in G1 and the cell cycle is completed.

The duration of the cell cycle varies between different cell types. In most mammalian cells it lasts between 10 and 30 hours. Cells in the first cell cycle phase (G1) do not always continue through the cycle. Instead they can exit from the cell cycle and enter a resting stage (G0).

A grand challenge in the post-genomic era is a complete computer representation of the cell, the organism, and the biosphere, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information. Towards this end a bioinformatics resource named KEGG as part of the research projects of the Kanehisa Laboratories in the Bioinformatics Center of Kyoto University and the Human Genome Center of the University of Tokyo.

KEGG (Kyoto Encyclopedia of Genes and Genomes) connects known information on molecular interaction networks, such as pathways and complexes (this is the Pathway Database). The KEGG database was initiated by the Japanese human genome programme in 1995 and is part of the Kyoto Encyclopedia of Genes and Genomes. According to the developers they consider KEGG to be a "computer representation" of the biological system. The KEGG database can be utilized for modeling and simulation, browsing and retrieval of data. It is a part of the systems biology approach.

There are 7 mammals, whose Cell Cycle Pathway is reported in KEGG. It is found that, 76 genes involved in cell cycle of Homo sapiens , Mus musculus, Rattus norvegicus, Pan troglodytes, Bos Taurus, Canis familiaris and Sus scrofa.When we go to find the information about these genes, we found molecular information for 73 gene in homo sapiens, 72 gene in Mus musculus, 69 gene in Rattus norvegicus, 55 gene in Pan troglodytes, 49 gene in Bos Taurus, 69 gene in Canis familiaris, 8 gene in Sus scrofa.

Hence, the Motive and Goal of this project entitled “Comparative Analysis of Cell Cycle Genes of Homo Sapiens, Mus musculus, Rattus norvegicus, Pan troglodytes, Bos Taurus, Canis familiaris, Sus Scrofa” is clear why we consider these 7 mammals and what we are going to analyze. So, to find-out the information about these uncharacterized genes in cell cycle of these organisms we use comparative analysis apparoach to find the sequences (based on similarity), and determine their functionality. We use various tools and databases through out this project.

Entrez Gene ( www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene ) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available. Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.

OMIM : Online Mendelian Inheritance in Man. This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information and references. It also contains copious links to MEDLINE and sequence records in the Entrez system, and links to additional related resources at NCBI and elsewhere.

HPRD : The Human Protein Reference Database is a protein database accessible through internet. This resource depicts information on human protein functions including protein-protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. Protein annotation information that is catalogued was derived through manual curation using published literature by expert biologists and through bioinformatics analyses of the protein sequence.

PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins.

UniProtKB/Swiss-Prot is a manually annotated protein knowledgebase established in 1986 and maintained since 2003 by the UniProt Consortium, a collaboration between the Swiss Institute of Bioinformatics (SIB) and the Department of Bioinformatics and Structural Biology of the Geneva University, the European Bioinformatics Institute (EBI) and the Georgetown University Medical Center's Protein Information Resource (PIR).

GeneCards database is developed and maintained in the Crown Human Genome Center at the Weizmann Institute of Science in Israel. Founded in 1997, the GeneCards project defined as its goal to integrate the fragments of information scattered over a variety of specialized databases into a coherent picture.

ProDom is a protein domain family database constructed automatically by clustering homologous segments. The ProDom building procedure MKDOM2 is based on recursive PSI-BLAST searches. The source protein sequences are non-fragmentary sequences derived from SWISS-PROT and TrEMBL databases. ProDom was first established in 1993 and maintained by the Laboratoire de Génétique Cellulaire and the Laboratoire de Interactions Plantes-Microorganismes (INRA/CNRS) in Toulouse. It is now maintained by the PRABI (bioinformatics center of Rhone-Alpes). The ProDom database consists of domain family entries. Each entry provides a multiple sequence alignment of homologous domains and a family consensus sequence.

BLAST : The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

UniGene : An Organized View of the Transcriptome. Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.

Microsoft Office Access : previously known as Microsoft Access , is a relational database management system from Microsoft which combines the relational Microsoft Jet Database Engine with a graphical user interface. It is a member of the 2007 Microsoft Office system. We used Microsoft Access because Access can use data stored in Access/Jet, Microsoft SQL Server, Oracle, or any ODBC-compliant data container.

Microsoft Internet Information Services (IIS; formerly called Server) is a set of Internet-based services for servers using Microsoft Windows. It is the world's second most popular web server in terms of overall websites. As of September 2007 it served 34.94% of all websites and 36.63% of all active websites according to Netcraft. The servers currently include FTP, SMTP, NNTP, and HTTP/HTTPS.

NOTE : Microsoft Internet Information Services (IIS) is the main competitor to Apache, trailed by Sun Microsystems' Sun Java System Web Server and a host of other applications such as Zeus Web Server.

On the basis of the comparative analysis approach we putatively determine all genes in cell cycle except 3 genes; Mps1, Bub2, MEN because these genes are not reported in KEGG or any other database, and we are not able to find similarity of these genes with any other gene available in databases.