Yıl 2013, Cilt 37, Sayı 5, Sayfalar 547 - 555 2014-05-16

Global assessment of network inference algorithms based on available literature of gene/protein interactions
Global assessment of network inference algorithms based on available literature of gene/protein interactions

Gökmen ALTAY [1] , Nejla ALTAY [2] , David NEAL [3]

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We propose a framework that uses the available gene/protein interaction databases of the literature as a universal benchmark in order to globally assess the inference performances of gene network inference algorithms. We also developed an R software package for convenient use of the framework, which can also be used in general as a quick tool to search in the literature for available validations of interactions. We applied the proposed approach to 2 publicly available prostate cancer gene expression datasets and a large breast cancer gene expression dataset. The results revealed different aspects and superiority of algorithms that had not been compared previously in the available literature. Our approach allowed the assessing and comparing of the algorithms on a real dataset of a size of around 30,000 probes, which showed the strengths and weaknesses of the algorithms from different points of view rather than conventional approaches. We further show that our approach provides a unique advantage in assessing the performance of an inference method when applied to a new dataset and thus sheds light on the results of a de novo application, which would be obscure without our approach.
We propose a framework that uses the available gene/protein interaction databases of the literature as a universal benchmark in order to globally assess the inference performances of gene network inference algorithms. We also developed an R software package for convenient use of the framework, which can also be used in general as a quick tool to search in the literature for available validations of interactions. We applied the proposed approach to 2 publicly available prostate cancer gene expression datasets and a large breast cancer gene expression dataset. The results revealed different aspects and superiority of algorithms that had not been compared previously in the available literature. Our approach allowed the assessing and comparing of the algorithms on a real dataset of a size of around 30,000 probes, which showed the strengths and weaknesses of the algorithms from different points of view rather than conventional approaches. We further show that our approach provides a unique advantage in assessing the performance of an inference method when applied to a new dataset and thus sheds light on the results of a de novo application, which would be obscure without our approach.
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Yazar: Gökmen ALTAY

Yazar: Nejla ALTAY

Yazar: David NEAL

Bibtex @ { tbtkbiology139559, journal = {Turkish Journal of Biology}, issn = {1300-0152}, eissn = {1303-6092}, address = {TÜBİTAK}, year = {2014}, volume = {37}, pages = {547 - 555}, doi = {10.3906/biy-1210-8}, title = {Global assessment of network inference algorithms based on available literature of gene/protein interactions}, key = {cite}, author = {ALTAY, Nejla and ALTAY, Gökmen and NEAL, David} }
APA ALTAY, G , ALTAY, N , NEAL, D . (2014). Global assessment of network inference algorithms based on available literature of gene/protein interactions. Turkish Journal of Biology, 37 (5), 547-555. DOI: 10.3906/biy-1210-8
MLA ALTAY, G , ALTAY, N , NEAL, D . "Global assessment of network inference algorithms based on available literature of gene/protein interactions". Turkish Journal of Biology 37 (2014): 547-555 <http://dergipark.gov.tr/tbtkbiology/issue/11690/139559>
Chicago ALTAY, G , ALTAY, N , NEAL, D . "Global assessment of network inference algorithms based on available literature of gene/protein interactions". Turkish Journal of Biology 37 (2014): 547-555
RIS TY - JOUR T1 - Global assessment of network inference algorithms based on available literature of gene/protein interactions AU - Gökmen ALTAY , Nejla ALTAY , David NEAL Y1 - 2014 PY - 2014 N1 - doi: 10.3906/biy-1210-8 DO - 10.3906/biy-1210-8 T2 - Turkish Journal of Biology JF - Journal JO - JOR SP - 547 EP - 555 VL - 37 IS - 5 SN - 1300-0152-1303-6092 M3 - doi: 10.3906/biy-1210-8 UR - http://dx.doi.org/10.3906/biy-1210-8 Y2 - 2018 ER -
EndNote %0 Turkish Journal of Biology Global assessment of network inference algorithms based on available literature of gene/protein interactions %A Gökmen ALTAY , Nejla ALTAY , David NEAL %T Global assessment of network inference algorithms based on available literature of gene/protein interactions %D 2014 %J Turkish Journal of Biology %P 1300-0152-1303-6092 %V 37 %N 5 %R doi: 10.3906/biy-1210-8 %U 10.3906/biy-1210-8
ISNAD ALTAY, Gökmen , ALTAY, Nejla , NEAL, David . "Global assessment of network inference algorithms based on available literature of gene/protein interactions". Turkish Journal of Biology 37 / 5 (Mayıs 2014): 547-555. http://dx.doi.org/10.3906/biy-1210-8