Thyroid Meta-Analysis

The following files accompany a paper published in JCO:

Obi L. Griffith, Adrienne Melck, Steven J.M. Jones and Sam M. Wiseman. 2006. A Meta-analysis and Meta-review of Thyroid Cancer Gene Expression Profiling Studies Identifies Important Diagnostic Biomarkers. Journal of Clinical Oncology. 24(31):5043-5051.

 

All zip archives contain a README file explaining their contents.
Files can be browsed directly from the downloads directory or from the links below.

• Overlap analysis mapping files (zip)
  • Files used to map published lists of differentially expressed genes (from accession, probe id, SAGE tag, etc) to a common gene identifier (Entrez Gene ID)
• P-value analysis mapping files (zip)
  • Files used to map total gene lists for each expression technology (Affymetrix HG-U133A, SAGE, etc) to a common gene identifier (Entrez Gene ID) for Monte Carlo simulation
• P-value analysis total gene files (zip)
  • Final total gene lists (after mapping to Entrez) for each expression technology used in Monte Carlo simulation
• DChip Affymetrix subset analysis files (zip)
  • All files used in DChip re-analysis of 5 sets of raw Affymetrix data (Cel files) for comparison to our 'meta-review' method.
• Cancer versus non-cancer breakdown analysis (zip)
  • Files providing gene lists for breakdown of 'cancer vs. non-cancer' into 'cancer vs. normal' and 'cancer vs. benign'.
• Overlap analysis results - gene detail files (zip)
  • Detailed results of overlap overlap analysis for all genes and for all comparison groups
  • Individual comparison groups available below (click 'details' link for comparison group of interest)
  • See details README file for explanation of column headings
• Overlap analysis results - gene summary files (zip)
  • Summarized results of overlap overlap analysis for all genes and for all comparison groups
  • Individual comparison groups available below (click 'summary' link for comparison group of interest)
  • See summary README file for explanation of column headings

Suppl. Data Table 1. Overlap analysis results by comparison group
(details README | summary README)

Comparison group	Condition set 1	Condition set 2	# comparisons	# genes (multi-study confirmation)
All comparisons details	Any	Any	34
Cancer vs. non-cancer details | summary	ACL, ATC, FCL, FTC, FVPTC, HCC, M, MACL, PCL, PTC, TCVPTC, UCL	AFTN, CTN, FA, GT, HN, Norm	21	755 (107)
Cancer vs. normal details | summary	ACL, ATC, FCL, FTC, FVPTC, HCC, M, MACL, PCL, PTC, TCVPTC, UCL	Norm	12	478 (53)
Cancer vs. benign details | summary	ACL, ATC, FCL, FTC, FVPTC, HCC, M, MACL, PCL, PTC, TCVPTC, UCL	AFTN, CTN, FA, GT, HN	8	332 (38)
Normal vs. benign details | summary	Norm	AFTN, CTN, FA, GT, HN	3	19 (1)
Papillary vs. non-cancer details | summary	FVPTC, PCL, PTC, TCVPTC	AFTN, CTN, FA, GT, HN, Norm	12	503 (82)
Papillary cancer vs. normal details | summary	FVPTC, PCL, PTC, TCVPTC	Norm	8	369 (49)
Papillary cancer vs. benign details | summary	FVPTC, PCL, PTC, TCVPTC	AFTN, CTN, FA, GT, HN	4	183 (13)
Papillary cancer vs. other details | summary	FVPTC, PCL, PTC, TCVPTC	Any other	15	528 (107)
FVPTC vs. other details | summary	FVPTC	Any other	2	157 (0)
FTC vs. FA details | summary	FTC	FA	6	222 (3)
Follicular cancer vs. other details | summary	FTC, FCL	Any other	10	403 (15)
Aggressive vs. other details | summary	ACL, ATC, M, MACL	Any other	4	145 (4)
Anaplastic cancer vs. other details | summary	ACL, ATC, MACL	Any other	3	91 (6)

Supplementary data table 1. The following table provides detailed and summarized results for all comparison groups considered in our meta-review/meta-analysis. A comparison group refers to a list of comparisons that address a common question of interest. For example, to identify markers that consistently distinguish cancer from non-cancer (normal or benign) we would analyze all the comparisons that contrast ‘cancer’ samples (i.e. PTC, FTC, ATC, etc) against ‘non-cancer’ samples (i.e. Norm, GT, FA, etc). Genes are then ranked according to several criteria in the following order of importance: (1) Number of comparisons in agreement (i.e. listing the same gene as differentially expressed and with a consistent direction of change); (2) Total number of samples for comparisons in agreement; and (3) Average fold change reported for comparisons in agreement. The 'details' file provides all data upon which this analysis was performed (e.g. study/comparison reporting the gene, original gene identifier, mapping method, fold change, etc). Entries are sorted by Entrez ID. The summary file summarizes the amount of overlap observed for each gene and orders the genes according to our ranking scheme. Please read the details README or summary README for more information on these file formats.