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Cancer Genome Characterization Initiative

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NCI/Affymetrix Human Transcriptome Project

The Human Transcriptome Project

Affymetrix, in collaboration with the National Cancer Institute, initiated the Human Transcriptome Project (HTP) in 2001 to generate the complete collection of transcribed elements of the human genome. Traditionally, researchers studying the transcriptome focused on the coding part of the genome. However, early findings from the HTP demonstrate that more than an order of magnitude of the genome is transcribed than can be accounted for by the predicted and characterized exons. These novel RNAs are believed to have important structural and regulatory functions and, as a consequence, any alteration in their sequence or level of expression can, as with coding RNA, contribute to cancer.


The goals of the HTP are to find the complete sites of:
  • Transcription
  • Transcription factor binding
  • Chromatin modification
  • DNA methylation
  • Chromosomal origins of replication

View Transcriptome Data

Data from Phase I (chromosomes 21 & 22) of the HTP can be viewed on the UCSC Genome Browser. In the "position" field, enter the chromosome number and location. Once the view is loaded, select "dense" in the "Transcriptome" track to summarize the data, or "full" for the expanded data set.

Project History

The project history can be summarized briefly:
  • The initial pilot study, Phase I, generated transcription maps for Chromosomes 21 and 22 using tiling arrays interrogating the chromosomes at a resolution of 35 base pairs (Kapranov et al, 2002; Kapranov et al, 2003; Kampa et al, 2004). Binding sites for the proximal transcription factors Sp1, c-myc, and p53 have been mapped onto the chromosomes (Cawley et al, 2004).
  • Phase II of the project has generated transcription maps for approximately 30% of the human genome (chromosomes 6, 7, 13, 14, 19, 20, 21, 22, X, and Y) at a higher resolution of 5 base pairs. The data is in the process of being analyzed.
  • Phase III of the project will generate analogous data for the remaining 70% of the human genome. Attempts will be made to integrate other transcriptome information.

Publications and Supplementary Data

  1. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SPA, and Gingeras TR, (2002). Large-Scale Transcriptional Activity in Chromosomes 21 and 22. Science 296:916-919. Supplementary data

  2. Kapranov P, Sementchenko VI, and Gingeras TR. (2003) Beyond Expression Profiling: Next generation uses of high density oligonucleotide arrays. Briefings in Functional Genomics and Proteomics: Volume 2 Number 1:47-56.

  3. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko VI, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, and Gingeras TR, (2004). Unbiased Mapping of Transcription Factor Binding Sites Along Human Chromosomes 21 and 22 Points to Widespread Regulation of Non-Coding RNAs. Cell 116:499-511. Supplementary data.

  4. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley SE, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, and Gingeras TR, (2004). Novel RNAs Identified from an In-depth Analysis of the Transcriptome of Human Chromosomes 21 and 22. Genome Research 14:331-342.

  5. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR, (2005). Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution. Science. 2005 Mar 24; [Epub ahead of print]. Supplemental data