Analysis Report Available Offline

A major goal of Metascape is to facilitate communication by presenting bioinformatics analysis results in a way that is easily interpretable to biology users.  More specifically, Metascape presents data in an article-style web page called Analysis Report (Figure 1).

Figure 1.  Metascape presents analysis results in a PowerPoint presentation, a conditionally-formatted Excel spreadsheet, a Zip package containing all data files and publication-quality graphics.  Most of all, all these files are accessible through an article-like Analysis Report web page.

Analysis Report includes details for Results, Materials & Methods, Figures, Tables, and References sections.  Based on feedback, this is an extremely appreciated format for presenting data.  In addition, Analysis Report web page also contains links at the very top of the page to a number of additional files to further facilitate communication:

(1) An Excel file, where tabular data are conditionally-formatted and gene candidates can be easily sorted and filtered based on 1/0 binary columns.  Many publications use the spreadsheet output as journal supplementary files.

(2) A PowerPoint presentation, where slides include key visualizations to help users share findings.  Each slide also contains detailed explanations in the note session, so user can interpret the graphics better and be prepared to answer technical questions from their audience.

(3) All data files and figures are packaged into a Zip file.  Figures include publication-quality formats such as PDF or SVG formats, or formats that can be further manipulated by third-party tools (such as Cytoscape).  So far, 61% of the publications citing Metascape include graphics as figures, making it self-evident that these graphics are indeed interpretable and publication ready.

To protect your data privacy and to also avoid complicated login process, Metascape tags each of your analysis request with a randomly-generated session ID and the Analysis Report can be retrieved by the associated URL for three days.  Although the Zip file can be downloaded and stored locally, the Analysis Report itself are only available online.  After three days, session results are deleted, users would need to reanalyze the data in order to produce the Analysis Report again.

With the latest update (Jan 30, 2018), the Zip package now contains an AnalysisReport.html file as well.  This means users can now download the Zip package, unzip it into a folder, then open to read the AnalysisReport.html file offline in a browser.

In short, Analysis Report can now be stored locally and be shared with others!  We hope you like it.

Watch out gene symbols within Excel

We do not recommend use gene symbols (or synonyms) as primary identifier within a gene list, especially within Excel. Excel irreversibly converts certain symbols into dates and it becomes much worse when gene synonyms are used.

We checked all primary human gene symbols, Excel automatically converts the following 35 symbols into dates: FEB1, FEB2, FEB5, FEB6, FEB7, FEB9, FEB10, MARCH1, MARC1, MARCH2, MARC2, MARCH3, MARCH4, MARCH5, MARCH6, MARCH7, MARCH8, MARCH9, MARCH10, MARCH11, SEPT1, SEPT2, SEPT3, SEPT4, SEPT5, SEPT6, SEPT7, SEPT8, SEPT9, SEPT10, SEPT11, SEPT12, SEPT14, SEP15, DEC1.

The conversion is irreversible for two reasons.  First, the original symbol is lost and the cell only stores an integer representing the number of days since Jan 1, 1900.  Second, notice both MARCH1 and MARC1 map to the same date, as well as MARCH2 and MARC2.

The situation become even worse, if we allow gene synonyms.  E.g., SEP53 (Gene ID 49860) becomes Sep, 1953, 2E4 (Gene ID 11133) becomes 20000. 9-27 (Gene ID 8519) becomes Sep 27th.

It is a wild west, when we look into mouse and rat.  There are primary symbols such as 201E9, 9130022E09, 3e46, NA, NaN, etc.

How to fix a gene symbol in Excel? To enter MARCH1 into a cell, type 'MARCH1 (prefix it with a single quote). This hints Excel to preserve the input, while the single quote is nicely invisible to Excel formula and in data export.

For all the reasons above, we recommend other gene identifier types to be used with Excel.  Metascape supports Entrez Gene ID, RefSeq, UniProt, Ensembl and UCSC identifiers, which all work peacefully with Excel.