Docolon+cancer+gene+PTPRJ+and+potential+genomic+implications+in+other+organisms

Does the linked colon cancer gene PTPRJ have any genomic implications in other organisms?

Wiki created by Robin E. Renzi Email: rei36@unh.edu Genomics, Proteomics and Bioinformatics Fall 2010 UNHM

PTPRJ Background Information and recent groundbreaking developments Applied Genomic Tools Used to Inquire about Hypothesis = **~** Locate this Gene Using Map Viewer................. PTPRJ Mapviewer = =**~** Protein Algorithm Analysis Using BLASTp Program....... PTPRJ BLASTp Program = =**~** Alignment Using Geneious...................... PTPRJ Alignment = =**~** Phylogenetic Trees & Bootstrap Analysis Using MEGA 5 Beta 4.......... PTPRJ Phylogenetic Trees =

Annotated Bibliography


 * 1. [|Endocrinology] Iuliano R, Palmieri D, He H, Iervolino A, Borbone E, Pallante P, Cianflone A, Nagy R, Alder H, Calin GA, Trapasso F, Giordano C, Croce CM, de la Chapelle A,Fusco A. (2010). Role of PTPRJ genotype in papillary thyroid carcinoma risk. Endocrine-Related Cancer.17(4):1001-6. This article was used to establish supporting evidence of PTPRJ in connection with thyroid carcinoma.


 * 2. [|Oncogenetics] Ruivenkamp, C., et al (2003). LOH of //PTPRJ// occurs early in colorectal cancer and is associated with chromosomal loss of 18q12–21. Oncogene; Division of Molecular Genetics. 22, 3472-3474. This article was used to collect information that supported the hypothesis that PTPRJ was a predictor of colorectal cancer.

> Other Designations: CD148 antigen; DEP-1; HPTP eta; R-PTP-J; density-enhanced phosphatase 1; human density enhanced phosphatase-1; protein tyrosine phosphatase, receptor type, J polypeptide; protein-tyrosine phosphatase eta; protein-tyrosine phosphatase receptor type J; receptor-type tyrosine-protein phosphatase eta; susceptibility to colon cancer 1, mouse, homolog of Chromosome: 11; Location: 11p11.2 Annotation: Chromosome 11NC_000011.9 (48002110..48192394) MIM: 600925 ID: 5795 > This article was used to gather summary gene and lineage information on PTPRJ.
 * 3. [|Entrez Gene] Official Symbol: PTPRJ and Name: protein tyrosine phosphatase, receptor type, J[Homo sapiens] Other Aliases: CD148, DEP1, HPTPeta, R-PTP-ETA, SCC1

Genomics Tools Bibliography


 * [|http://www.ncbi.nlm.nih.gov/projects/mapview] Map Viewer is used to show the location of PTPRJ on Chromosome 11 with other known genes and phenotypes in this area.
 * [] Map Viewer shows all Homo sapien chromosomes and where relative on Chromosme 11 PTPRJ is located which is just above the centromere.
 * [] This program, Basic Local Alignment Search Tool uses known algorithms to find similarities between amino acid sequences. A BLASTp specifically looks at amino acid sequeces of proteins, whereas BLASTn uses nucleotide bases to conduct inqueries.
 * [] A genomic tool, MEGA 5 Beta 4 is designed for conducting automatic and manual sequence alignments, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
 * [] Geneious is a bioinformatics tool that allows for organization of large volumes of genomic data and analysis.
 * [] Follow the history of PTPRJ from pre-historic eras to current day existence using the taxonomy browser.