A bioinformatics analysis of protein tyrosine phosphatases in humans

T. K.B. Gandhi, Sreenath Chandran, Suraj Peri, R. Saravana, Ramars Amanchy, T. S.Keshava Prasad, Akhilesh Pandey

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Protein tyrosine phosphatases (PTPs) cooperate with protein tyrosine kinases to regulate signal transduction pathways. Genome-wide surveys cataloging protein tyrosine phosphatases in humans have recently been carried out. Here, we present a bioinformatics analysis of protein tyrosine phosphatases in the human genome to examine their domain architecture, alternative splicing and pseudogenes. We present evidence that alternative transcripts exist for 25 out of 35 PTPs analyzed. These alternative transcripts include novel exons; skipped exons as well as cryptic donor/acceptor splice sites. We discovered a novel isoform of PTPN18 based on analysis of expressed sequence tags (ESTs). The deletion of 4 exons in the catalytic domain of the novel isoform may alter the enzymatic activity toward its substrates. We were able to experimentally validate 2 of our novel isoform predictions through RT-PCR. Finally, a user-friendly web-based resource that consolidates the gene and protein annotations for all human protein tyrosine phosphatases has been developed and is freely available at http://ptpr.ibioinformatics.org.

Original languageEnglish (US)
Pages (from-to)79-89
Number of pages11
JournalDNA Research
Volume12
Issue number2
DOIs
StatePublished - Sep 27 2005
Externally publishedYes

Fingerprint

Protein Tyrosine Phosphatases
Computational Biology
Molecular Sequence Annotation
Exons
Protein Isoforms
RNA Splice Sites
Cataloging
Pseudogenes
Expressed Sequence Tags
Alternative Splicing
Human Genome
Protein-Tyrosine Kinases
Signal Transduction
Catalytic Domain
Genome
Polymerase Chain Reaction
Proteins

Keywords

  • Alternative splicing
  • Comparative genomics
  • Genomics
  • Signal transduction
  • Tyrosine phosphorylation

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Gandhi, T. K. B., Chandran, S., Peri, S., Saravana, R., Amanchy, R., Prasad, T. S. K., & Pandey, A. (2005). A bioinformatics analysis of protein tyrosine phosphatases in humans. DNA Research, 12(2), 79-89. https://doi.org/10.1093/dnares/12.2.79

A bioinformatics analysis of protein tyrosine phosphatases in humans. / Gandhi, T. K.B.; Chandran, Sreenath; Peri, Suraj; Saravana, R.; Amanchy, Ramars; Prasad, T. S.Keshava; Pandey, Akhilesh.

In: DNA Research, Vol. 12, No. 2, 27.09.2005, p. 79-89.

Research output: Contribution to journalArticle

Gandhi, TKB, Chandran, S, Peri, S, Saravana, R, Amanchy, R, Prasad, TSK & Pandey, A 2005, 'A bioinformatics analysis of protein tyrosine phosphatases in humans', DNA Research, vol. 12, no. 2, pp. 79-89. https://doi.org/10.1093/dnares/12.2.79
Gandhi TKB, Chandran S, Peri S, Saravana R, Amanchy R, Prasad TSK et al. A bioinformatics analysis of protein tyrosine phosphatases in humans. DNA Research. 2005 Sep 27;12(2):79-89. https://doi.org/10.1093/dnares/12.2.79
Gandhi, T. K.B. ; Chandran, Sreenath ; Peri, Suraj ; Saravana, R. ; Amanchy, Ramars ; Prasad, T. S.Keshava ; Pandey, Akhilesh. / A bioinformatics analysis of protein tyrosine phosphatases in humans. In: DNA Research. 2005 ; Vol. 12, No. 2. pp. 79-89.
@article{989b07d0d1ac461db177cd40d7614234,
title = "A bioinformatics analysis of protein tyrosine phosphatases in humans",
abstract = "Protein tyrosine phosphatases (PTPs) cooperate with protein tyrosine kinases to regulate signal transduction pathways. Genome-wide surveys cataloging protein tyrosine phosphatases in humans have recently been carried out. Here, we present a bioinformatics analysis of protein tyrosine phosphatases in the human genome to examine their domain architecture, alternative splicing and pseudogenes. We present evidence that alternative transcripts exist for 25 out of 35 PTPs analyzed. These alternative transcripts include novel exons; skipped exons as well as cryptic donor/acceptor splice sites. We discovered a novel isoform of PTPN18 based on analysis of expressed sequence tags (ESTs). The deletion of 4 exons in the catalytic domain of the novel isoform may alter the enzymatic activity toward its substrates. We were able to experimentally validate 2 of our novel isoform predictions through RT-PCR. Finally, a user-friendly web-based resource that consolidates the gene and protein annotations for all human protein tyrosine phosphatases has been developed and is freely available at http://ptpr.ibioinformatics.org.",
keywords = "Alternative splicing, Comparative genomics, Genomics, Signal transduction, Tyrosine phosphorylation",
author = "Gandhi, {T. K.B.} and Sreenath Chandran and Suraj Peri and R. Saravana and Ramars Amanchy and Prasad, {T. S.Keshava} and Akhilesh Pandey",
year = "2005",
month = "9",
day = "27",
doi = "10.1093/dnares/12.2.79",
language = "English (US)",
volume = "12",
pages = "79--89",
journal = "DNA Research",
issn = "1340-2838",
publisher = "Oxford University Press",
number = "2",

}

TY - JOUR

T1 - A bioinformatics analysis of protein tyrosine phosphatases in humans

AU - Gandhi, T. K.B.

AU - Chandran, Sreenath

AU - Peri, Suraj

AU - Saravana, R.

AU - Amanchy, Ramars

AU - Prasad, T. S.Keshava

AU - Pandey, Akhilesh

PY - 2005/9/27

Y1 - 2005/9/27

N2 - Protein tyrosine phosphatases (PTPs) cooperate with protein tyrosine kinases to regulate signal transduction pathways. Genome-wide surveys cataloging protein tyrosine phosphatases in humans have recently been carried out. Here, we present a bioinformatics analysis of protein tyrosine phosphatases in the human genome to examine their domain architecture, alternative splicing and pseudogenes. We present evidence that alternative transcripts exist for 25 out of 35 PTPs analyzed. These alternative transcripts include novel exons; skipped exons as well as cryptic donor/acceptor splice sites. We discovered a novel isoform of PTPN18 based on analysis of expressed sequence tags (ESTs). The deletion of 4 exons in the catalytic domain of the novel isoform may alter the enzymatic activity toward its substrates. We were able to experimentally validate 2 of our novel isoform predictions through RT-PCR. Finally, a user-friendly web-based resource that consolidates the gene and protein annotations for all human protein tyrosine phosphatases has been developed and is freely available at http://ptpr.ibioinformatics.org.

AB - Protein tyrosine phosphatases (PTPs) cooperate with protein tyrosine kinases to regulate signal transduction pathways. Genome-wide surveys cataloging protein tyrosine phosphatases in humans have recently been carried out. Here, we present a bioinformatics analysis of protein tyrosine phosphatases in the human genome to examine their domain architecture, alternative splicing and pseudogenes. We present evidence that alternative transcripts exist for 25 out of 35 PTPs analyzed. These alternative transcripts include novel exons; skipped exons as well as cryptic donor/acceptor splice sites. We discovered a novel isoform of PTPN18 based on analysis of expressed sequence tags (ESTs). The deletion of 4 exons in the catalytic domain of the novel isoform may alter the enzymatic activity toward its substrates. We were able to experimentally validate 2 of our novel isoform predictions through RT-PCR. Finally, a user-friendly web-based resource that consolidates the gene and protein annotations for all human protein tyrosine phosphatases has been developed and is freely available at http://ptpr.ibioinformatics.org.

KW - Alternative splicing

KW - Comparative genomics

KW - Genomics

KW - Signal transduction

KW - Tyrosine phosphorylation

UR - http://www.scopus.com/inward/record.url?scp=24944507990&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=24944507990&partnerID=8YFLogxK

U2 - 10.1093/dnares/12.2.79

DO - 10.1093/dnares/12.2.79

M3 - Article

C2 - 16303740

AN - SCOPUS:24944507990

VL - 12

SP - 79

EP - 89

JO - DNA Research

JF - DNA Research

SN - 1340-2838

IS - 2

ER -