Open Access Research article

Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries

Nelson JF Silveira1, Leonardo Varuzza2, Ariane Machado-Lima3, Marcelo S Lauretto2, Daniel G Pinheiro4, Rodrigo V Rodrigues56, Patrícia Severino7, Francisco G Nobrega8, Head and Neck Genome Project GENCAPO9, Wilson A Silva4, Carlos A de B Pereira2* and Eloiza H Tajara56*

Author Affiliations

1 Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, UNIVAP, São José dos Campos, SP, Brazil

2 Instituto de Matemática e Estatística, USP, São Paulo, SP, Brazil

3 BIOINFO-USP Núcleo de Pesquisas em Bioinformática, USP, SP, Brazil

4 Departamento de Genética, Faculdade de Medicina de Ribeirão Preto-USP, Centro de Terapia Celular, Centro Regional de Hemoterapia, SP, Brazil

5 Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, FAMERP, São José do Rio Preto, SP, Brazil

6 Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, USP, São Paulo, SP, Brazil

7 Instituto de Ensino e Pesquisa Albert Einstein, São Paulo, SP, Brazil

8 Departamento de Biociências e Diagnóstico Bucal, Faculdade de Odontologia, UNESP, São José dos Campos, SP, Brazil

9 Complete authors list and addresses is presented in the Appendix

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BMC Medical Genomics 2008, 1:56  doi:10.1186/1755-8794-1-56

Published: 11 November 2008

Additional files

Additional file 1:

Supplementary Table 1. Tags with different frequencies between larynx SAGE libraries according to the criteria described in the Materials and Methods section.

Supplementary Table 2. A total of 8,979 tags expressed in the N+ tumor SAGE library.

Supplementary Table 3. A total of 17,588 tags expressed in the N0 tumor SAGE library.

Supplementary Table 4. A total of 15,102 tags expressed in the control SAGE library.

Supplementary Table 5. A total of 12,229 tags expressed in at least two SAGE libraries.

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Additional file 2:

Supplementary Table 6. Sixty top-up regulated tags in aggressive versus non-aggressive larynx library.

Supplementary Table 7. Sixty top-down regulated tags in aggressive versus non-aggressive larynx library.

Supplementary Table 8. Sixty top-up regulated tags in aggressive versus normal larynx library.

Supplementary Table 9. Sixty top-down regulated tags in aggressive versus normal larynx library.

Supplementary Table 10. Sixty top-up regulated tags in non-aggressive versus normal larynx library.

Supplementary Table 11. Sixty top-down regulated tags in non-aggressive versus normal larynx library.

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Additional file 3:

Supplementary Table 12. Discrepancies between Kemp and chi-square analysis of SAGE data set.

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