Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

Purvesh Khatri; Marina Sirota; Atul J. Butte

doi:10.1371/journal.pcbi.1002375

Loading metrics

Open Access

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

Purvesh Khatri ,

* E-mail: pkhatri@stanford.edu (PK); abutte@stanford.edu (AJB)

Affiliations Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America, Lucile Packard Children's Hospital, Palo Alto, California, United States of America
⨯
Marina Sirota,

Affiliations Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America, Lucile Packard Children's Hospital, Palo Alto, California, United States of America
⨯
Atul J. Butte

* E-mail: pkhatri@stanford.edu (PK); abutte@stanford.edu (AJB)

Affiliations Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America, Lucile Packard Children's Hospital, Palo Alto, California, United States of America
⨯

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

Purvesh Khatri,
Marina Sirota,
Atul J. Butte

Published: February 23, 2012
https://doi.org/10.1371/journal.pcbi.1002375

Reader Comments

Post a new comment on this article

Check out this paper

Posted by bionaz on 22 Jun 2012 at 15:29 GMT

We wish we could see your review before have our paper accepted for publication! Many of the limitations we have described in our paper to justify the need for a new method are well reviewed here. The method that we proposed in our paper (A Novel Dynamic Impact Approach (DIA) for Functional Analysis of Time-Course Omics Studies: Validation Using the Bovine Mammary Transcriptome, PLoS ONE) seems to account for several of the limitations pointed out by the authors.
Thanks for putting this together!

Competing interests declared: I am author of the cited paper.

Subject Areas
?

For more information about PLOS Subject Areas, click here.
We want your feedback. Do these Subject Areas make sense for this article? Click the target next to the incorrect Subject Area and let us know. Thanks for your help!

Genome annotation
Is the Subject Area "Genome annotation" applicable to this article?

Thanks for your feedback.
Gene expression
Is the Subject Area "Gene expression" applicable to this article?

Thanks for your feedback.
Apoptosis
Is the Subject Area "Apoptosis" applicable to this article?

Thanks for your feedback.
Human genomics
Is the Subject Area "Human genomics" applicable to this article?

Thanks for your feedback.
Microarrays
Is the Subject Area "Microarrays" applicable to this article?

Thanks for your feedback.
Proteomic databases
Is the Subject Area "Proteomic databases" applicable to this article?

Thanks for your feedback.
Pseudogenes
Is the Subject Area "Pseudogenes" applicable to this article?

Thanks for your feedback.
Genome analysis
Is the Subject Area "Genome analysis" applicable to this article?

Thanks for your feedback.

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

Reader Comments

Post Your Discussion Comment

Why should this posting be reviewed?

Thank You!

Check out this paper

Posted by bionaz on 22 Jun 2012 at 15:29 GMT