Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha

Luigi Scotto¹ , Gopeshwar Narayan¹^,2 , Subhadra V Nandula¹ , Shivakumar Subramaniyam¹ , Andreas M Kaufmann³ , Jason D Wright⁴ , Bhavana Pothuri⁴^,5 , Mahesh Mansukhani¹ , Achim Schneider³ , Hugo Arias-Pulido⁶^,7 and Vundavalli V Murty¹^,8^,9

¹Department of Pathology, Columbia University Medical Center, New York, New York, USA

²Department of Molecular & Human Genetics, Banaras Hindu University, Varanasi, India

³Department of Gynecology, Charité Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany

⁴Gynecologic Oncology, Columbia University Medical Center, New York, New York, USA

⁵Department of Gyenecologic Oncology, New York University Medical Center, New York, New York, USA

⁶Division of Hematology/Oncology, The University of New Mexico Cancer Center, 900 Camino de Salud NE, Albuquerque, New Mexico, USA

⁷Department of Tumor Molecular Biology, Instituto Nacional de Cancerología, Bogotá, Colombia

⁸Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, USA

⁹Irving Cancer Research Center, Room 605, Columbia University Medical Center, 1130 St. Nicholas Ave, New York, New York 10032, USA

author email corresponding author email

Molecular Cancer 2008, 7:58doi:10.1186/1476-4598-7-58


Published:	17 June 2008

Additional files

Additional file 1:

Chromosome summary plot of inferred copy number gain and loss in cervical cancer. Chromosomes marked by solid vertical lines with dotted lines separating short arm (left) and long arm (right). Each SNP value at more than 3 and less than 1 were plotted on horizontal line to show the frequency of gains (above, in red) and losses (below, in blue). Chromosome 5 is highlighted, where 5p gain ranks 1st as the most commonly gained chromosome in cervical cancer.

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Additional file 2:

Clinical and histologic information of CC cases used in SNP, gene expression, and FISH analysis. Specimens used for various types of tests.

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Additional file 3:

Supervised analyses of gene expression profile of chromosome 5 genes identified by comparing and filtering between normal cervix and cervical cancer. In the matrix, each row represents the gene expression relative to group mean and each column represents a sample (shown on Top). T, represents primary tumor; CL, represents cell line. The dendrogram on left shows unsupervised clustering of genes differentially expressed between normal vs. tumor. The dendrogram on top shows unsupervised clustering of tumor and normal. The scale bar (-2 to +2) on the bottom represents the level of expression with intensities of blue represents decrease and red for increase in expression.

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Additional file 4:

Supervised analysis of 26 over expressed genes enriched to identify 5p genes by filtering all over expressed probe sets on chromosome 5 against all 5p probes on U133A array between tumor and normal. In the matrix, each row represents the gene expression relative to group mean and each column represents a sample (shown on Top). T, represents primary tumor; CL, represents cell line. The dendrogram on left shows unsupervised clustering of genes differentially expressed between tumor and normal. The names of genes are shown on right. The scale bar (-2 to +2) on the bottom represents the level of expression with intensities of blue represents decrease and red for increase in expression. The groups within tumors shown at top represent no gain of chromosome 5p (I) and 5p gain (II).

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Additional file 5:

Supervised analysis of 17 genes significantly down regulated on 5q in cervical cancer compared to normal cervix. Down-regulated genes on 5q were identified by filtering all probe sets on chromosome 5q present on U133A array between tumor and normal. In the matrix, each row represents the gene expression relative to group mean and each column represents a sample (shown on Top). T, represents primary tumor; CL, represents cell line. The dendrogram on left shows unsupervised clustering of genes differentially expressed between tumor and normal. The names of genes are shown on right. The scale bar (-2 to +2) on the bottom represents the level of expression with intensities of blue represents decrease and red for increase in expression. The groups within tumors shown at top represent no loss of chromosome 5q (I) and 5q loss (II). Note no significant differences were found between 5q deleted tumors vs. undeleted tumors.

Format: TIFF Size: 1.5MB Download file