| Introduction for gastric cancer datasets |
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- The next section (Browse PATHOME-drug results for gastric cancer datasets) includes the PATHOME-drug result links for the 8 gastric cancer datasets represented in our manuscript (submitted). All datasets were generated separately from Gene Expression Omnibus (GEO), and focused on several aspects of gastric cancer. Here is a brief description of the below table.
- GSE accession (JobID) : GSE accession number of each dataset, and result job ID for the analysis using each dataset
- Group specification : Describes which characteristic of the dataset we focused
- No. of samples : Number of samples of the deposited dataset
- Running time : How long the analysis using PATHOME-drug taken
- The last section shows the PATHOME-drug result for the TCGA gastric cancer dataset. A detailed description on the dataset can be found in the 'How to prepare input data from big data repository (TCGA dataset) in user's own preferences' section in the help page.
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| Browse PATHOME-drug results for GEO gastric cancer datasets |
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Run times, PATHOME-drug result pages and input file examples for various gastric cancer (GC) datasets. To measure the running time distribution, we applied PATHOME-drug to eight GC datasets, divided into the two groups indicated in the column 'Group specification', and measured the processing time. 'c1' and 'c2' represent the two nominal group names.
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| GSE accession | (PATHOME-drug result page) | [Input file example] | log2-
transformed? | Group specification | No. of probes | No. of samples | Running time |
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| GSE15459 | (0324033527) | [Input file example] | No | Diffuse (c1) vs. Intestinal (c2) | 21,051 | 40 (c1) vs. 35 (c2) | 13.88 min |
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| GSE37023 | (0324023355) | [Input file example] | Yes | Normal (c1) vs. tumors (c2) | 13,213 | 39 (c1) vs. 112 (c2) | 16.65 min |
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| GSE13861 | (0324020415) | [Input file example] | Yes | Adjacent normal (c1) vs. tumors (c2) | 36,159 | 19 (c1) vs. 65 (c2) | 21.55 min |
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| GSE15081 | (0330042215) | [Input file example] | Yes | Peritoneal relapse (c1) vs. relapse-free (c2) | 14,540 | 38 (c1) vs. 18 (c2) | 12.02 min |
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| GSE27342 | (0324015452) | [Input file example] | No | Adjacent normal (c1) vs. tumors (c2) | 21,374 | 80 (c1) vs. 80 (c2) | 44.72 min |
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| GSE47007 | (0324034304) | [Input file example] | No | Diffuse (c1) vs. Intestinal (c2) | 9,079 | 12 (c1) vs. 18 (c2) | 7.78 min |
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| GSE63089 | (0324125153) | [Input file example] | Yes | Adjacent normal (c1) vs. tumors (c2) | 17,170 | 45 (c1) vs. 45 (c2) | 53.95 min |
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| GSE36968 | (0328123836) | [Input file example] | Yes | Noncancerous gastric tissues (c1) vs. tumors (c2) | 18,892 | 6 (c1) vs. 24 (c2) | 30 min |
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| Browse PATHOME-drug result for TCGA gastric cancer dataset |
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| Task definition: In the given G2 grade, One group is <= 45-year old, and the other group is > 85-year old. Users make a proper input file by using Excel. This section contains the result of Supplementary Method 1.
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All rights reserved to BIBS laboratory, Seoul National University, Korea.
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