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Predicting central genes in protein-protein interaction network during mouse fibroblast to cardiomyocyte conversion

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Year: 2014
COI code: CIGS13_1206
Paper Language: English

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Authors Predicting central genes in protein-protein interaction network during mouse fibroblast to cardiomyocyte conversion

  Abdulshakour Mohammadnia - National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran These authors contributed equally to this work.
  Moein Yaqubi - National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran These authors contributed equally to this work.
  Niusha Khazaei - National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran These authors contributed equally to this work.
  Hossein Fallahi - Department of Biology, School of Science, Razi University, Kermanshah, Iran -Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran

Abstract:

Postnatal heart fibroblasts convert to induced cardiomyocyte using combination of transcription factors. Expression pattern of genes change during direct reprogramming of mouse fibroblast to cardiomyocyte. We use system biology tools to find central genes in protein-protein interaction during direct conversion of mouse fibroblast into cardiomyocyte.Method: Data with GSE number 22292 were obtained from GEO database. RMA algorithm was used to raw data normalization. DEgenes were selected using fold change algorithm. DE genes functional clustering done using DAVID database. Interactionof DE genes with other proteins was determined using AgilentLiteratureSearch plugin and STRING database. Cytoscapewas used to construction of protein-protein interaction network. In order to detect central genes of network, degree parameter of CentiScaPe was applied to whole network. Result: We compare gene expression profile of week 2 cells versus week 4 ones and show 91 genes differentially expressedbetween these two groups of cells. Functional clustering analysis of DE genes using DAVID database shows several termssuch as signaling, glycoprotein and glycosylation as member of cluster with highest enrichment score. We construct proteinprotein interaction network of DE genes and the best network contains 45 nodes and 107 edges. In our study CCL2, PLAU, ACTN2, BGN, CCL9, SERPINE1, LOX, MYL1, CCL12 and CCL7 are the central genes during conversion of fibroblastinto cardiomyocyte based on degree parameter. Notably we find that 8 out of 10 of these genes contribute in signaling term,while ACTN2 and MYL1 is not. Conclusion: Identification of these central genes may lead to improve efficiency of this conversion

Keywords:

Differential expressed genes, direct reprogramming, fibroblast, cardiomyocyte

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COI code: CIGS13_1206

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Mohammadnia, Abdulshakour; Moein Yaqubi; Niusha Khazaei & Hossein Fallahi, 2014, Predicting central genes in protein-protein interaction network during mouse fibroblast to cardiomyocyte conversion, 12th Congress of Iranian Genetics Society, تهران, انجمن ژنتيك ايران, https://www.civilica.com/Paper-CIGS13-CIGS13_1206.htmlInside the text, wherever referred to or an achievement of this article is mentioned, after mentioning the article, inside the parental, the following specifications are written.
First Time: (Mohammadnia, Abdulshakour; Moein Yaqubi; Niusha Khazaei & Hossein Fallahi, 2014)
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