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.
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.
Helena
H
Brentani
Otávia L
OL
Caballero
Anamaria A
AA
Camargo
Aline M
AM
da Silva
Wilson Araújo
WA
da Silva
Emmanuel
E
Dias Neto
Marco
M
Grivet
Arthur
A
Gruber
Pedro Edson Moreira
PE
Guimaraes
Winston
W
Hide
Christian
C
Iseli
C Victor
CV
Jongeneel
Janet
J
Kelso
Maria Aparecida
MA
Nagai
Elida Paula Benquique
EP
Ojopi
Elisson C
EC
Osorio
Eduardo M R
EM
Reis
Gregory J
GJ
Riggins
Andrew John George
AJ
Simpson
Sandro
S
de Souza
Brian J
BJ
Stevenson
Robert L
RL
Strausberg
Eloiza H
EH
Tajara
Sergio
S
Verjovski-Almeida
Marcio Luis
ML
Acencio
Mário Henrique
MH
Bengtson
Fabiana
F
Bettoni
Walter F
WF
Bodmer
Marcelo R S
MR
Briones
Luiz Paulo
LP
Camargo
Webster
W
Cavenee
Janete M
JM
Cerutti
Luis Eduardo
LE
Coelho Andrade
Paulo César
PC
Costa dos Santos
Maria Cristina
MC
Ramos Costa
Israel Tojal
IT
da Silva
Marcos Roberto H
MR
Estécio
Karine
K
Sa Ferreira
Frank B
FB
Furnari
Milton
M
Faria
Pedro A F
PA
Galante
Gustavo S
GS
Guimaraes
Adriano Jesus
AJ
Holanda
Edna Teruko
ET
Kimura
Maarten R
MR
Leerkes
Xin
X
Lu
Rui M B
RM
Maciel
Elizabeth A L
EA
Martins
Katlin Brauer
KB
Massirer
Analy S A
AS
Melo
Carlos Alberto
CA
Mestriner
Elisabete Cristina
EC
Miracca
Leandro Lorenco
LL
Miranda
Francisco G
FG
Nobrega
Paulo S
PS
Oliveira
Apua C M
AC
Paquola
José Rodrigo C
JR
Pandolfi
Maria Ines de Moura
MI
Campos Pardini
Fabio
F
Passetti
John
J
Quackenbush
Beatriz
B
Schnabel
Mari Cleide
MC
Sogayar
Jorge E
JE
Souza
Sandro R
SR
Valentini
Andre C
AC
Zaiats
Elisabete Jorge
EJ
Amaral
Liliane A T
LA
Arnaldi
Amelia Goes
AG
de Araújo
Simone Aparecida
SA
de Bessa
David C
DC
Bicknell
Maria Eugenia
ME
Ribeiro de Camaro
Dirce Maria
DM
Carraro
Helaine
H
Carrer
Alex F
AF
Carvalho
Christian
C
Colin
Fernando
F
Costa
Cyntia
C
Curcio
Ismael Dale Cotrim
ID
Guerreiro da Silva
Neusa
N
Pereira da Silva
Márcia
M
Dellamano
Hamza
H
El-Dorry
Enilza Maria
EM
Espreafico
Ari José
AJ
Scattone Ferreira
Cristiane
C
Ayres Ferreira
Maria Angela H Z
MA
Fortes
Angelita Habr
AH
Gama
Daniel
D
Giannella-Neto
Maria Lúcia C C
ML
Giannella
Ricardo R
RR
Giorgi
Gustavo Henrique
GH
Goldman
Maria Helena S
MH
Goldman
Christine
C
Hackel
Paulo Lee
PL
Ho
Elza Myiuki
EM
Kimura
Luiz Paulo
LP
Kowalski
Jose E
JE
Krieger
Luciana C C
LC
Leite
Ademar
A
Lopes
Ana Mercedes S C
AM
Luna
Alan
A
Mackay
Suely Kazue Nagahashi
SK
Mari
Adriana Aparecida
AA
Marques
Waleska K
WK
Martins
André
A
Montagnini
Mario
M
Mourão Neto
Ana Lucia T O
AL
Nascimento
A Munro
AM
Neville
Marina P
MP
Nobrega
Mike J
MJ
O'Hare
Audrey Yumi
AY
Otsuka
Anna Izabel
AI
Ruas de Melo
Maria Luisa
ML
Paco-Larson
Gonçalo
G
Guimarães Pereira
Neusa
N
Pereira da Silva
Joao Bosco
JB
Pesquero
Juliana Gilbert
JG
Pessoa
Paula
P
Rahal
Claudia Aparecida
CA
Rainho
Vanderlei
V
Rodrigues
Silvia Regina
SR
Rogatto
Camila Malta
CM
Romano
Janaina Gusmao
JG
Romeiro
Benedito Mauro
BM
Rossi
Monica
M
Rusticci
Renata
R
Guerra de Sá
Simone Cristina
SC
Sant' Anna
Miriam L
ML
Sarmazo
Teresa Cristina de Lima E
TC
Silva
Fernando Augusto
FA
Soares
Maria de Fátima
Mde F
Sonati
Josane
J
de Freitas Sousa
Diana
D
Queiroz
Valéria
V
Valente
André Luiz
AL
Vettore
Fabiola Elizabeth
FE
Villanova
Marco Antonio
MA
Zago
Heloisa
H
Zalcberg
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