A comprehensive transcript index of the human genome generated using microarrays and computational approaches.
BACKGROUND
Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from approximately 50,000 known and predicted transcript sequences from the human genome were used to survey transcription from a diverse set of 60 tissues and cell lines using ink-jet microarrays. Further, expression activity over at least six conditions was more generally assessed using genomic tiling arrays consisting of probes tiled through a repeat-masked version of the genomic sequence making up chromosomes 20 and 22.


RESULTS
The combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts. This set of high-confidence transcripts represents the first experimentally driven annotation of the human genome. In addition, the results from genomic tiling suggest that a large amount of transcription exists outside of annotated regions of the genome and serves as an example of how this activity could be measured on a genome-wide scale.


CONCLUSIONS
These data represent one of the most comprehensive assessments of transcriptional activity in the human genome and provide an atlas of human gene expression over a unique set of gene predictions. Before the annotation of the human genome is considered complete, however, the previously unannotated transcriptional activity throughout the genome must be fully characterized.
Schadt
Eric E
EE
Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA. eric_schadt@merck.com
Edwards
Stephen W
SW
GuhaThakurta
Debraj
D
Holder
Dan
D
Ying
Lisa
L
Svetnik
Vladimir
V
Leonardson
Amy
A
Hart
Kyle W
KW
Russell
Archie
A
Li
Guoya
G
Cavet
Guy
G
Castle
John
J
McDonagh
Paul
P
Kan
Zhengyan
Z
Chen
Ronghua
R
Kasarskis
Andrew
A
Margarint
Mihai
M
Caceres
Ramon M
RM
Johnson
Jason M
JM
Armour
Christopher D
CD
Garrett-Engele
Philip W
PW
Tsinoremas
Nicholas F
NF
Shoemaker
Daniel D
DD
D002890:Chromosomes, Human, Pair 20 / Q000235:genetics; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014158:Transcription, Genetic / Q000235:genetics*