Evidence map›Paper›PMID 19088187›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2008

Genome-wide analysis of cancer/testis gene expression.

Oliver Hofmann, Otavia L Caballero, Brian J Stevenson, Yao-Tseng Chen, Tzeela Cohen, Ramon Chua, Christopher A Maher, Sumir Panji, Ulf Schaefer, Adele Kruger and 7 more

Open access · bronzeAbstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 212 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
212citing papers in PubMed, 1 pooled it
5.0field-weighted citation impact, top 4% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

212 citing papers in PubMed, 1 synthesis or guideline pooled it, 336 citations in OpenAlex.

  1. Pooled it
  2. Cancer regression and neurological toxicity following anti-MAGE-A3 TCR gene therapy.Journal of immunotherapy (Hagerstown, Md. : 1997) · 2013
    Trial
  3. Trial
  4. Trial
  5. Review
  6. Review
  7. Article
  8. Review
  9. Article
  10. Review
  11. Article
  12. Article
  13. Review
  14. Article
  15. Review
  16. IncreasedPharmaceuticals (Basel, Switzerland) · 2024
    Article
  17. Article
  18. Article
  19. Article
  20. Review

152 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors at 6 institutions in 4 countries.

Oliver HofmannDepartment of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, SPH2, 4th Floor, Boston, MA 02115, USA. ohofmann@hsph.harvard.edu
Otavia L Caballero
Brian J Stevenson
Yao-Tseng Chen
Tzeela Cohen
Ramon Chua
Christopher A Maher
Sumir Panji
Ulf Schaefer
Adele Kruger
Minna Lehvaslaiho
Piero Carninci
Yoshihide Hayashizaki
C Victor Jongeneel
Andrew J G Simpson
Lloyd J Old
Winston Hide
Memorial Sloan Kettering Cancer Center · USUniversity of the Western Cape · ZAHarvard University · USSIB Swiss Institute of Bioinformatics · CHWako University · JPCornell University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Cancer/Testis (CT) genes, normally expressed in germ line cells but also activated in a wide range of cancer types, often encode antigens that are immunogenic in cancer patients, and present potential for use as biomarkers and targets for immunotherapy. Using multiple in silico gene expression analysis technologies, including twice the number of expressed sequence tags used in previous studies, we have performed a comprehensive genome-wide survey of expression for a set of 153 previously described CT genes in normal and cancer expression libraries. We find that although they are generally highly expressed in testis, these genes exhibit heterogeneous gene expression profiles, allowing their classification into testis-restricted (39), testis/brain-restricted (14), and a testis-selective (85) group of genes that show additional expression in somatic tissues. The chromosomal distribution of these genes confirmed the previously observed dominance of X chromosome location, with CT-X genes being significantly more testis-restricted than non-X CT. Applying this core classification in a genome-wide survey we identified >30 CT candidate genes; 3 of them, PEPP-2, OTOA, and AKAP4, were confirmed as testis-restricted or testis-selective using RT-PCR, with variable expression frequencies observed in a panel of cancer cell lines. Our classification provides an objective ranking for potential CT genes, which is useful in guiding further identification and characterization of these potentially important diagnostic and therapeutic targets.

Indexed as

Genome, HumanTestisA Kinase Anchor ProteinsCell Line, TumorChromosomes, HumanChromosomes, Human, XComputational BiologyGene Expression ProfilingGenomicsGPI-Linked ProteinsHomeodomain ProteinsHumansMaleMembrane ProteinsTesticular NeoplasmsAKAP4 protein, humanA Kinase Anchor ProteinsGPI-Linked ProteinsHomeodomain ProteinsMembrane ProteinsOTOA protein, humanRHOXF2 protein, human

Identifiers

PMID19088187
PMCPMC2603434
OpenAlexW1999042146

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.