Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks

نویسندگان

  • Yungang Xu
  • Maozu Guo
  • Xiaoyan Liu
  • Chunyu Wang
  • Yang Liu
  • Guojun Liu
چکیده

Module identification is a frequently used approach for mining local structures with more significance in global networks. Recently, a wide variety of bilayer networks are emerging to characterize the more complex biological processes. In the light of special topological properties of bilayer networks and the accompanying challenges, there is yet no effective method aiming at bilayer module identification to probe the modular organizations from the more inspiring bilayer networks. To this end, we proposed the pseudo-3D clustering algorithm, which starts from extracting initial non-hierarchically organized modules and then iteratively deciphers the hierarchical organization of modules according to a bottom-up strategy. Specifically, a modularity function for bilayer modules was proposed to facilitate the algorithm reporting the optimal partition that gives the most accurate characterization of the bilayer network. Simulation studies demonstrated its robustness and outperformance against alternative competing methods. Specific applications to both the soybean and human miRNA-gene bilayer networks demonstrated that the pseudo-3D clustering algorithm successfully identified the overlapping, hierarchically organized and highly cohesive bilayer modules. The analyses on topology, functional and human disease enrichment and the bilayer subnetwork involved in soybean fat biosynthesis provided both the theoretical and biological evidence supporting the effectiveness and robustness of pseudo-3D clustering algorithm.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

iSubgraph: Integrative Genomics for Subgroup Discovery in Hepatocellular Carcinoma Using Graph Mining and Mixture Models

The high tumor heterogeneity makes it very challenging to identify key tumorigenic pathways as therapeutic targets. The integration of multiple omics data is a promising approach to identify driving regulatory networks in patient subgroups. Here, we propose a novel conceptual framework to discover patterns of miRNA-gene networks, observed frequently up- or down-regulated in a group of patients ...

متن کامل

A review on the prevalent fabrication methods, microstructural, mechanical properties, and corrosion resistance of nanostructured hydroxyapatite containing bilayer and multilayer coatings used in biomedical applications

Surface treatments of the biomaterials are of great interest in many biomedical applications. Hydroxyapatite is a favorable candidate for surface modification of the implants. To date, a wide variety of methods have been developed to produce bio-active/biocompatible coatings with desirable features in order to improve the performance of the implants. This paper strives to overview the present p...

متن کامل

Novel attributes of steep-slope staggered type heterojunction p-channel electron-hole bilayer tunnel field effect transistor

In this paper, the electrical characteristics and sensitivity analysis of staggered type p-channel heterojunction electron-hole bilayer tunnel field effect transistor (HJ-EHBTFET) are thoroughly investigated via simulation study. The minimum lattice mismatch between InAs/GaAs0.1Sb0.9 layers besides low carrier effective mass of materials provides high probability ...

متن کامل

Morphology-controllable 1D-3D nanostructured TiO2 bilayer photoanodes for dye-sensitized solar cells.

Morphology-controlled bilayer TiO(2) nanostructures consisting of one-dimensional (1D) nanowire bottom arrays and a three-dimensional (3D) dendritic microsphere top layer were synthesized via a one-step hydrothermal method. These novel 1D-3D bilayer photoanodes demonstrated the highest energy conversion efficiency of 7.2% for rutile TiO(2) dye-sensitized solar cells to date, with TiCl(4) post-t...

متن کامل

Development and evaluation of regioselective bilayer floating tablets of Atenolol and Lovastatin for biphasic release profile

This study was performed to design bilayer regioselective floating tablets of atenolol and lovastatin to give immediate release of lovastatin and sustained release of atenolol. Bilayer floating tablets comprised two layers, i.e immediate release and controlled release layers. The immediate release layer comprised sodium starch glycollate as a super disintegrant and the sustained release layer c...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره 44  شماره 

صفحات  -

تاریخ انتشار 2016