Ben Gurion University of the Negev
Department of Computer Science

 

 


 

Gene bi-targeting by viral and human miRNAs


 
Isana Veksler-Lublinsky1 , Yonat Shemer-Avni2 ,  Klara Kedem1, Michal Ziv-Ukelson1

 

1 Department of Computer Science, Ben-Gurion University, 84105 Beer Sheva, Israel

2 Virology and Developmental Genetics/Health Sciences, Ben-Gurion University, 84105 Beer Sheva, Israel

 

Our method consists of two stages:

 

1. A target prediction stage: performs all against all dynamic programming on two sets of sequences (miRNAs and mRNAs) in order to predict, for every miRNA in the set, its target mRNAs.

 

The code for target prediction is available here.

 

2. A module search stage: looks for modules that are enriched in some biological process, using the results from the first stage and information from Gene Ontology and the miRNA Atlas.

 

A list of predicted modules: All modules

The predicted modules with details (the files are partitioned by GO categories):

See  example file.

Apoptosis:

1.      Induction_of_apoptosis

2.      Positive_regulation_of_apoptosis

3.      Induction_of_apoptosis_by_extracellular_signals

Signal Transduction

4.      Regulation_of_Rho_protein_signal_transduction

5.      Small_GTPase_mediated_signal_transduction

6.      Ras_protein_signal_transduction

7.      Regulation_of_small_GTPase_mediated_signal_transduction

8.      Regulation_of_Ras_protein_signal_transduction

9.      Negative_regulation_of_signal_transduction

10.  Rho_protein_signal_transduction

Cell Cycle/Cell Growth

11.  Meiotic_cell_cycle

12.  Cell_cycle_checkpoint

13.  M_phase_of_mitotic_cell_cycle

14.  Cell_growth

15.  Negative_regulation_of_cell_growth

16.  Angiogenesis

Cytokines/Caspases

17.  Cytokine_biosynthetic_process

18.  Regulation_of_caspase_activity

19.  Positive_regulation_of_caspase_activity

20.  Cytokine_production

21.  Regulation_of_cytokine_production

Proliferation

22.  Regulation_of_ lymphocyte_proliferation

23.  Lymphocyte_proliferation

24.  Positive_regulation_of_cell_proliferation

Immune response

25.  Immune_response

26.  Regulation_of_lymphocyte_activation

27.  Lymphocyte_activation

 

 

 

 

For more details about the method and results please refer to:

Isana Veksler-Lublinsky, Yonat Shemer-Avni, Klara Kedem and Michal Ziv-Ukelson. Gene bi-targeting by viral and human miRNAs. BMC Bioinformatics 11:249, 2010.

 

 

For more details, please contact

vaksler@cs.bgu.ac.il