The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.
Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define approximately 23,500 genes, of which only approximately 1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that <1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.
Brentani
Helena
H
Laboratorio de Genética Molecular do Cancer, Departmento de Radiologia, Universidade de São Paulo, Travessa da Rua Dr. Ovídeo Pires de Campos S/N, 4deg, Brazil.
Caballero
Otávia L
OL
Camargo
Anamaria A
AA
da Silva
Aline M
AM
da Silva
Wilson Araújo
WA
Dias Neto
Emmanuel
E
Grivet
Marco
M
Gruber
Arthur
A
Guimaraes
Pedro Edson Moreira
PE
Hide
Winston
W
Iseli
Christian
C
Jongeneel
C Victor
CV
Kelso
Janet
J
Nagai
Maria Aparecida
MA
Ojopi
Elida Paula Benquique
EP
Osorio
Elisson C
EC
Reis
Eduardo M R
EM
Riggins
Gregory J
GJ
Simpson
Andrew John George
AJ
de Souza
Sandro
S
Stevenson
Brian J
BJ
Strausberg
Robert L
RL
Tajara
Eloiza H
EH
Verjovski-Almeida
Sergio
S
Acencio
Marcio Luis
ML
Bengtson
Mário Henrique
MH
Bettoni
Fabiana
F
Bodmer
Walter F
WF
Briones
Marcelo R S
MR
Camargo
Luiz Paulo
LP
Cavenee
Webster
W
Cerutti
Janete M
JM
Coelho Andrade
Luis Eduardo
LE
Costa dos Santos
Paulo César
PC
Ramos Costa
Maria Cristina
MC
da Silva
Israel Tojal
IT
Estécio
Marcos Roberto H
MR
Sa Ferreira
Karine
K
Furnari
Frank B
FB
Faria
Milton
M
Galante
Pedro A F
PA
Guimaraes
Gustavo S
GS
Holanda
Adriano Jesus
AJ
Kimura
Edna Teruko
ET
Leerkes
Maarten R
MR
Lu
Xin
X
Maciel
Rui M B
RM
Martins
Elizabeth A L
EA
Massirer
Katlin Brauer
KB
Melo
Analy S A
AS
Mestriner
Carlos Alberto
CA
Miracca
Elisabete Cristina
EC
Miranda
Leandro Lorenco
LL
Nobrega
Francisco G
FG
Oliveira
Paulo S
PS
Paquola
Apua C M
AC
Pandolfi
José Rodrigo C
JR
Campos Pardini
Maria Ines de Moura
MI
Passetti
Fabio
F
Quackenbush
John
J
Schnabel
Beatriz
B
Sogayar
Mari Cleide
MC
Souza
Jorge E
JE
Valentini
Sandro R
SR
Zaiats
Andre C
AC
Amaral
Elisabete Jorge
EJ
Arnaldi
Liliane A T
LA
de Araújo
Amelia Goes
AG
de Bessa
Simone Aparecida
SA
Bicknell
David C
DC
Ribeiro de Camaro
Maria Eugenia
ME
Carraro
Dirce Maria
DM
Carrer
Helaine
H
Carvalho
Alex F
AF
Colin
Christian
C
Costa
Fernando
F
Curcio
Cyntia
C
Guerreiro da Silva
Ismael Dale Cotrim
ID
Pereira da Silva
Neusa
N
Dellamano
Márcia
M
El-Dorry
Hamza
H
Espreafico
Enilza Maria
EM
Scattone Ferreira
Ari José
AJ
Ayres Ferreira
Cristiane
C
Fortes
Maria Angela H Z
MA
Gama
Angelita Habr
AH
Giannella-Neto
Daniel
D
Giannella
Maria Lúcia C C
ML
Giorgi
Ricardo R
RR
Goldman
Gustavo Henrique
GH
Goldman
Maria Helena S
MH
Hackel
Christine
C
Ho
Paulo Lee
PL
Kimura
Elza Myiuki
EM
Kowalski
Luiz Paulo
LP
Krieger
Jose E
JE
Leite
Luciana C C
LC
Lopes
Ademar
A
Luna
Ana Mercedes S C
AM
Mackay
Alan
A
Mari
Suely Kazue Nagahashi
SK
Marques
Adriana Aparecida
AA
Martins
Waleska K
WK
Montagnini
André
A
Mourão Neto
Mario
M
Nascimento
Ana Lucia T O
AL
Neville
A Munro
AM
Nobrega
Marina P
MP
O'Hare
Mike J
MJ
Otsuka
Audrey Yumi
AY
Ruas de Melo
Anna Izabel
AI
Paco-Larson
Maria Luisa
ML
Guimarães Pereira
Gonçalo
G
Pereira da Silva
Neusa
N
Pesquero
Joao Bosco
JB
Pessoa
Juliana Gilbert
JG
Rahal
Paula
P
Rainho
Claudia Aparecida
CA
Rodrigues
Vanderlei
V
Rogatto
Silvia Regina
SR
Romano
Camila Malta
CM
Romeiro
Janaina Gusmao
JG
Rossi
Benedito Mauro
BM
Rusticci
Monica
M
Guerra de Sá
Renata
R
Sant' Anna
Simone Cristina
SC
Sarmazo
Miriam L
ML
Silva
Teresa Cristina de Lima E
TC
Soares
Fernando Augusto
FA
Sonati
Maria de Fátima
Mde F
de Freitas Sousa
Josane
J
Queiroz
Diana
D
Valente
Valéria
V
Vettore
André Luiz
AL
Villanova
Fabiola Elizabeth
FE
Zago
Marco Antonio
MA
Zalcberg
Heloisa
H
D002874:Chromosome Mapping; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015972:Gene Expression Regulation, Neoplastic; D014644:Genetic Variation; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D020543:Proteome; D012333:RNA, Messenger / Q000378:metabolism*; D014018:Tissue Distribution
D020543:Proteome; D012333:RNA, Messenger