iPathwayGuide Frequently-Asked Questions
iPathwayGuide supports analysis of Human, mouse, and rat. It supports the following files formats:
CuffDiff
DESeq
EdgeR
SAS/JMP Genomics
nSolver (NanoString Technologies)
Generic tab delimited .txt file (must contain gene symbol or uniprot ID, log2FC, p-value)
SCIEX SWATH 2.0 proteomics data files
Select Affymetrix CEL files*
*Supported Affy CEL Files may take several minutes to upload
Human
Human Genome U133
Human Genome U133A 2.0
Human Genome U133 Plus 2.0
Human Genome U95
Human Genome U35K
Mouse
Mouse Expression Set 430
Mouse Expression Set 430 2.0
Mouse Genome 430A 2.0
Rat
Rat Expression Set 230
Rat Genome 230 2.0
Rat Genome U34
Please make sure your are using the “…gene_exp.diff” file that comes from CuffLinks. There are some applications that claim to emulate CuffDiff output (e.g. Galaxy). If you are using one of these applications, please make sure the output file has all columns populated. See below for specific columns that must be present. Also, use this link to view the Cuffdiff manual.
| Column number | Column name | Example | Description |
|---|---|---|---|
| 1 | Tested id | XLOC_000001 | A unique identifier describing the transcipt, gene, primary transcript, or CDS being tested |
| 2 | gene | Lypla1 | The gene_name(s) or gene_id(s) being tested |
| 3 | locus | chr1:4797771-4835363 | Genomic coordinates for easy browsing to the genes or transcripts being tested. |
| 4 | sample 1 | Liver | Label (or number if no labels provided) of the first sample being tested |
| 5 | sample 2 | Brain | Label (or number if no labels provided) of the second sample being tested |
| 6 | Test status | NOTEST | Can be one of OK (test successful), NOTEST (not enough alignments for testing), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents testing. |
| 7 | FPKMx | 8.01089 | FPKM of the gene in sample x |
| 8 | FPKMy | 8.551545 | FPKM of the gene in sample y |
| 9 | log2(FPKMy/FPKMx) | 0.06531 | The (base 2) log of the fold change y/x |
| 10 | test stat | 0.860902 | The value of the test statistic used to compute significance of the observed change in FPKM |
| 11 | p | value 0.389292 | The uncorrected p-value of the test statistic |
| 12 | q | value 0.985216 | The FDR-adjusted p-value of the test statistic |
| 13 | significant | no | Can be either “yes” or “no”, depending on whether p is greater then the FDR after Benjamini-Hochberg correction for multiple-testing |
Generally, each analysis takes about 15 minutes to complete. If there are other analyses queued ahead of yours, it may take a bit longer. You will receive an email as soon as the analysis is complete.
It is a great idea to use the software and explore the capabilities before making a purchase. The way to do this is to create a free account on our web site www.advaitabio.com. Once you create an account, you will have full access to several analysis results. These datasets cover a range of experiment types, conditions, and analysis outcomes. You will be able to fully use the software to explore these data sets in whichever way you choose. You will have full access to interact with all of the demo analyses and experience all of the features of iPathwayGuide. We also provide sample data files, which will show you some of the formats that can be used to upload data for analysis. An alternative would be to setup a time and let one of us to show you around the software. You will learn more in a much shorter time, and you will also be able to get immediate answers to any questions you may have.
Here are the legends describing the symbols used on the pathway diagrams, gene networks and GO directed acyclic graph, respectively. Click an image for a larger view.
Yes! From the dashboard, just click share on any completed report. Then enter the email address for the person you wish to share it with. If they do not have an account, they will be prompted to create on. Once registered, they will be able to view the report.
We report the ‘Creation Time’ based on Coordinated Universal Time (UTC).
iPathwayGuide is designed to work with all the latest major browser platforms:
- Google Chrome
- Mozilla Firefox
- Apple Safari (Mac only, iOS not supported yet)
- Microsoft Internet Explorer 11 – Some image download capabilities may not function
iPathwayGuide works with the most popular differential expression files. Some 3rd party emulators (e.g. Galaxy) may structure their data slightly differently. Click on the sample files below to see the structure of these files.
Yes. From the login menu, click reset password. You will receive an email with the new password.
A list of databases and versions is available from within each report. See our Release Notes to see the latest data.
Citing iPathwayGuide
Using Advaita Bio’s products or content for any form of publication (e.g. print, electronically) requires researchers to cite them. Please use one of the options below for citations:
• “The Data (significantly impacted pathways, biological processes, molecular interactions, miRNAs, SNPs, etc.) were analyzed using Advaita Bio’s iPathwayGuide (https://www.advaitabio.com/ipathwayguide). This software analysis tool implements the ‘Impact Analysis’ approach that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc., as described in (Draghici, 2007, Tarca, 2008, Donato, 2013, Ahsan 2018).”
A systems biology approach for pathway level analysis
Analysis and correction of crosstalk effects in pathway analysis
A novel signaling pathway impact analysis
GEO2R does not perform normalization for Affymetrix CEL files. The Advaita iPathwayGuide CEL file uploader currently utilizes the Gene-chip Robust Multi-array Average (GCRMA) normalization method. As such, there can be discrepancies between CEL files processed with GEO2R vs. iPathwayGuide.