NCBI Projects with CGAP Data
Clone Registry
dbEST
Entrez GEO DataSets.
Gene Expression Omnibus
HomoloGene
Human BAC Resource
Gene
Map Viewer
SKY/CGH
Cancer Chromosomes
UniGene
UniSTS
|
|
Cancer Genome Anatomy Project
|
The Cancer Genome Anatomy Project (CGAP)
is an interdisciplinary
program established and administered by the National Cancer Institute
(NCI) to generate the information
and technological tools needed to decipher
the molecular anatomy of the cancer cell.
From CGAP's inception in 1996,
NCBI has been a key participant
in bioinformatics planning, data tracking, data archiving,
and analytical tool development and implementation. NCBI's role in CGAP has been
constantly evolving to meet the demands of changing and expanding raw
data sources, as well as the needs of the scientific community.
The information below highlights NCBI's contributions to CGAP.
NCBI collaborates closely with NCI as
the CGAP pipeline generates
large numbers of expressed sequence tags (EST), all of which
are deposited into
dbEST, and subsequently incorporated into
UniGene and
HomoloGene.
Gene-based, manual annotations may also be added via
Feedback for RefSeq and Entrez Gene.
"designing analytic tools"
|
NCBI created the first public CGAP website and
designed all analytical tools for the CGAP Tumor Gene
Index during the first four years of the project. Also,
NCBI offers analytic tools to infer gene expression information from our
extensive EST libraries. Gene expression profiles are linked to many of the
Unigene clusters (see
examples); in addition, there is a standalone tool
Digital Differential Display
to compare computed gene expression profiles between selected cDNA libraries.
The CGAP website provides other similar tools under Tissues.
"profiling gene expression"
|
Serial analysis of gene expression (SAGE)
is a more cost-efficient method of
producing gene expression data (compared to EST data). CGAP supports the
production of SAGE libraries and their sequencing while NCBI archives the SAGE libraries in the
Gene Expression Omnibus (GEO) database. These data are searchable using Entrez GEO DataSets.
"tracking biological reagents"
|
NCBI designed and continues to maintain
an internal database that tracks CGAP
samples, libraries and clones used in the generation of EST and SAGE data.
The wealth of data produced by CGAP has
lead NCBI and NCI staff to develop an ad hoc classification system of
hierarchically related keywords.
Both NCBI and NCI staff are responsible for the classification of all new human
and mouse EST libraries and SAGE libraries on a routine basis.
"mapping chromosome aberrations"
|
NCBI is collaborating closely with a component of CGAP called the
Cancer Chromosome Aberration Project (CCAP).
Using fluorescent in situ hybridization
(FISH), CCAP is generating clones that are spaced 1-2 Mb across the human genome.
Once mapped, these sequence-ready DNA BAC clones are then made available to
the research community. NCBI is involved in identifying candidate BAC clones to be
FISH-mapped, archiving the results, and localizing these clones onto draft
sequence contigs. This data can be viewed through NCBI's
Map Viewer,
is linked to NCBI's Clone Registry and
UniSTS
sites and can also be displayed synoptically on
NCI's CGAP Chromosome and
NCBI's Human BAC Resource
websites.
CCAP is also characterizing chromosome aberrations in
selected tumor types through the use of spectral karyotyping (SKY) and
comparative genomic hybridization (CGH). SKY facilitates identification
of chromosomal aberrations and CGH can be used to generate a map of
DNA copy number changes in tumor genomes. The
SKY/CGH database has been
designed to house this data, and is publicly accessible.
Drs. Mitelman, Mertens and Johansson have been
systematically summarizing recurrent neoplasia-associated
chromosomal aberrations from the
Mitelman Database of Chromosome Aberrations in Cancer. This work,
which originally appeared in the
April 1997 Special Issue of Nature Genetics, entitled
"A breakpoint map of recurrent chromosomal rearrangements in human neoplasia", is continuously
updated and a summary of the latest data can be viewed with
NCBI´s
Map Viewer. All recurrent aberrations can be interactively
queried at NCI's CGAP website at
Recurrent Chromosome Aberrations in Cancer.
The Cancer
Chromosomes database integrates the SKY/M-FISH & CGH Database with
the Mitelman Database of Chromosome Aberrations in Cancer and the Recurrent
Chromosome Aberrations in Cancer database. These three data sets can now be
searched seamlessly by use of the Entrez search and retrieval system for
chromosome aberrations, clinical data, and reference citations. Common
diagnoses, anatomic sites, chromosome breakpoints, junctions, numerical and
structural abnormalities, and bands gained and lost among selected cases can be
compared by use of the "similarity" report. Because the model used for CGH data
is a subset of the karyotype data, it is now possible to examine the
similarities between CGH results and karyotypes directly.
|