Virus Dataset Detail

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Dataset Information
Accession GSE55542
Status 2014/3/5
Title Gene expression profiling of HPV-active, HPV-inactive and HPV-negative oropharyngeal squamous cell carcinomas
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Approximately 25% of all head and neck cancers (HNC), and up to 60% of oropharyngeal cancers (OPC) are associated with human papillomavirus (HPV), predominantly HPV16. HPV-associated OPC have better prognosis and a more favorable response to therapy as compared to HPV-negative tumors. Viral oncoproteins are capable of transforming primary human keratinocytes from either genital or oral epithelia in vitro and most likely play the same role in vivo, by disrupting cell-cycle regulatory pathways leading to a genetic progression to ano-genital cancer and OPC. However, the precise mechanisms by which HPV mediates malignant transformation of keratinocytes in the upper digestive tract epithelia are not entirely clear. HPV E7-mediated inactivation of pRb results in overexpression of p16INK4A, which is commonly used as a clinical surrogate marker for HPV positivity/activity. However, high p16INK4A alone has insufficient sensitivity and specificity as a biomarker of HPV positivity in different mucosal sub-sites of HNC. Therefore, increasing emphasis is being placed on the assessment of viral load and E7 oncogene expression, resulting in further classification of HPV positive OPC as HPV-active and HPV-inactive. Differences in risk factors, age of presentation, clinical behavior and gene expression profiles indicate that HPV-positive and HPV-negative tumors develop via different molecular mechanisms and are biologically distinct. This study aimed to compare the gene expression profiles of HPV-active, -inactive and -negative OPC and determine their biological differences.
Samples
GSM ID Sample info Characteristics Description
GSM1338930 Analysis 1: HPV Active - Biological replicate 1 gender:Male; race:European American re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_4 sample in analysis 3, 5
GSM1338931 Analysis 1: HPV Active - Biological replicate 2 gender:Male; race:European American re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_2 sample in analysis 3, 5
GSM1338932 Analysis 1: HPV Active - Biological replicate 3 gender:Male; race:European American re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_4 sample in analysis 3, 5
GSM1338933 Analysis 1: HPV Active - Biological replicate 4 gender:Male; race:European American re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_1 sample in analysis 3, 5
GSM1338934 Analysis 1: HPV Active - Biological replicate 5 gender:Male; race:European American re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_4 sample in analysis 3, 5
GSM1338935 Analysis 1: HPV Active - Biological replicate 6 gender:Male; race:European American re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_2 sample in analysis 3, 5
GSM1338936 Analysis 1: HPV Active - Biological replicate 7 gender:Male; race:European American re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_3 sample in analysis 3, 5
GSM1338937 Analysis 1: HPV Active - Biological replicate 8 gender:Male; race:European American re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_4 sample in analysis 3, 5
GSM1338938 Analysis 1: HPV Active - Biological replicate 9 gender:Male; race:African American re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_1 sample in analysis 5
GSM1338939 Analysis 1: HPV Active - Biological replicate 10 gender:Male; race:European American re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_3 sample in analysis 3, 5
GSM1338940 Analysis 1: HPV Active - Biological replicate 11 gender:Male; race:European American re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_1 sample in analysis 3, 5
GSM1338941 Analysis 1: HPV Active - Biological replicate 12 gender:Male; race:European American re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_3 sample in analysis 3, 5
GSM1338942 Analysis 1: HPV Inactive - Biological replicate 1 gender:Female; race:European American re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_2 sample in analysis 3, 4, 7
GSM1338943 Analysis 1: HPV Inactive - Biological replicate 2 gender:Female; race:European American re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_4 sample in analysis 3, 4, 7
GSM1338944 Analysis 1: HPV Inactive - Biological replicate 3 gender:Female; race:European American re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_1 sample in analysis 3, 4, 7
GSM1338945 Analysis 1: HPV Inactive - Biological replicate 4 gender:Female; race:African American re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_2 sample in analysis 4
GSM1338946 Analysis 1: HPV Inactive - Biological replicate 5 gender:Female; race:African American re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_1 sample in analysis 4
GSM1338947 Analysis 1: HPV Inactive - Biological replicate 6 gender:Male; race:African American re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_2 sample in analysis 4
GSM1338948 Analysis 1: HPV Inactive - Biological replicate 7 gender:Male; race:African American re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_2 sample in analysis 4
GSM1338949 Analysis 1: HPV Inactive - Biological replicate 8 gender:Female; race:European American re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_4 sample in analysis 3, 4, 7
GSM1338950 Analysis 1: HPV Negative - Biological replicate 1 gender:Male; race:European American re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_1 sample in analysis 2, 3, 4, 6, 8
GSM1338951 Analysis 1: HPV Negative - Biological replicate 2 gender:Female; race:European American re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_2 sample in analysis 2, 3, 4, 6, 8
GSM1338952 Analysis 1: HPV Negative - Biological replicate 3 gender:Male; race:European American re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_3 sample in analysis 2, 3, 4, 6, 8
GSM1338953 Analysis 1: HPV Negative - Biological replicate 4 gender:Female; race:African American re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_4 sample in analysis 2, 4, 6
GSM1338954 Analysis 1: HPV Negative - Biological replicate 5 gender:Male; race:European American re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_1 sample in analysis 2, 3, 4, 6, 8
GSM1338955 Analysis 1: HPV Negative - Biological replicate 6 gender:Male; race:African American re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_2 sample in analysis 2, 4, 6
GSM1338956 Analysis 1: HPV Negative - Biological replicate 7 gender:Female; race:African American re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_3 sample in analysis 2, 4, 6
GSM1338957 Analysis 1: HPV Negative - Biological replicate 8 gender:Male; race:African American re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_4 sample in analysis 2, 4, 6
GSM1338958 Analysis 1: HPV Negative - Biological replicate 9 gender:Male; race:European American re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_1 sample in analysis 2, 3, 4, 6, 8
GSM1338959 Analysis 1: HPV Negative - Biological replicate 10 gender:Female; race:African American re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_3 sample in analysis 2, 4, 6
GSM1338960 Analysis 1: HPV Negative - Biological replicate 11 gender:Male; race:European American re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_3 sample in analysis 2, 3, 4, 6, 8
GSM1338961 Analysis 1: HPV Negative - Biological replicate 12 gender:Male; race:African American re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_3 sample in analysis 2, 4, 6
GSM1338962 Analysis 1: HPV Negative - Biological replicate 13 gender:Male; race:African American re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_4 sample in analysis 2, 4, 6
GSM1338963 Analysis 1: HPV Negative - Biological replicate 14 gender:Male; race:African American re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_1 sample in analysis 2, 4, 6
GSM1338964 Analysis 1: HPV Negative - Biological replicate 15 gender:Male; race:European American re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_3 sample in analysis 2, 3, 4, 6, 8
GSM1338965 Analysis 1: HPV Negative - Biological replicate 16 gender:Female; race:European American re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_3 sample in analysis 2, 3, 4, 6, 8
Platform GPL17077  : Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version)
Literature 25899179  
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* p<0.05 ** p<0.01