PageRank-based identification of signaling crosstalk from transcriptomics data: the case of Arabidopsis thaliana

Molecular BioSystems
Nooshin OmranianZoran Nikoloski

Abstract

The levels of cellular organization, from gene transcription to translation to protein-protein interaction and metabolism, operate via tightly regulated mutual interactions, facilitating organismal adaptability and various stress responses. Characterizing the mutual interactions between genes, transcription factors, and proteins involved in signaling, termed crosstalk, is therefore crucial for understanding and controlling cells' functionality. We aim at using high-throughput transcriptomics data to discover previously unknown links between signaling networks. We propose and analyze a novel method for crosstalk identification which relies on transcriptomics data and overcomes the lack of complete information for signaling pathways in Arabidopsis thaliana. Our method first employs a network-based transformation of the results from the statistical analysis of differential gene expression in given groups of experiments under different signal-inducing conditions. The stationary distribution of a random walk (similar to the PageRank algorithm) on the constructed network is then used to determine the putative transcripts interrelating different signaling pathways. With the help of the proposed method, we analyze a transcriptomics dat...Continue Reading

References

Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Jan 10, 2003·Nucleic Acids Research·Alvis BrazmaSusanna-Assunta Sansone
Dec 19, 2003·Nucleic Acids Research·David J CraigonSean May
Mar 18, 2005·The Plant Cell·Karin LjungGöran Sandberg
Apr 28, 2007·The Plant Journal : for Cell and Molecular Biology·Tamara GigolashviliUlf-Ingo Flügge
May 25, 2007·The Plant Journal : for Cell and Molecular Biology·Tamara GigolashviliUlf-Ingo Flügge
Apr 25, 2008·Bioinformatics·Yong LiDilip Rajagopalan
Dec 17, 2009·Plant Physiology·Manpreet S KatariRodrigo A Gutiérrez
Jan 1, 2010·The Plant Journal : for Cell and Molecular Biology·Ruslan YatusevichStanislav Kopriva
Mar 23, 2010·Trends in Plant Science·Ida E SønderbyBarbara A Halkier

❮ Previous
Next ❯

Citations

Oct 3, 2013·Journal of Experimental Botany·Grzegorz MoniuszkoAgnieszka Sirko
Oct 24, 2013·The Plant Journal : for Cell and Molecular Biology·Katharina GläserErwin Grill
Jan 30, 2015·Frontiers in Plant Science·Agnieszka SirkoPawel Sęktas

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.