A human PPI network has been reconstructed from eight databases [

A human PPI network has been reconstructed from eight databases [19]. This network is composed of 44,223 non-redundant PPIs among 9,520 different proteins, corresponding to 30% of the human proteome (the remaining proteins have no known cellular partners and, therefore, cannot be included in this network). Interestingly, HHBV are clearly over-represented in this H-H network (134 (92%) of the total HHBV). Analysis of the HHBV-HHBV sub-network (all connected 146 HHBV proteins), which is composed of 1,977 non-redundant PPIs among different HHBV and more interconnected than the H-H network, indicated that HBV proteins have a strong tendency to interact

with highly connected cellular proteins (Figure 1B, Additional file 1, Table S4). This also suggests that HBV preferentially BMN 673 order targets host proteins already known to be engaged in protein-protein interactions. Analysis of the relationship between hepatocellular carcinoma and HHBV In order to provide a global view of human proteins involved

in HCC associated with the HBV – with the aim of clarifying the relationship between HBV proteins and hepatocellular carcinoma-associated proteins (HHCC) – we also made use of NLP methods to extract literature related to HCC from PubMed. Using the LCZ696 solubility dmso keyword search [e.g., (liver cancer ""[title] OR”" hepatocellular carcinoma “”[title] OR”" Liver Neoplasm “”[title] OR”" Liver Neoplasms “”[title] AND (“” 1980/01/01 “”[PDAT] :”" 2009/01/01 “”[PDAT]))], we retrieved 19,050 related articles. Based on a combination of text mining procedures and expert curation, a total of 666 HHCC (number of PMID greater selleck kinase inhibitor than

or equal to 2) Oxalosuccinic acid were identified from 6,709 summary descriptions (Additional file 1, Table S5). Among these, nine of HHCC had more than 100 PMID references (Figure 2A). Figure 2 Analysis of the relationship between H HCC and H HBV . (A) Gene list of top nine HHCC. (B) Overlap between HHCC and HHBV. The blue area corresponds to HHBV; the yellow area, to HHCC: and the green area, to HHBV-HHCC. (C) Gene Ontology analysis of HHBV and HHBV-HHCC. Compared with HHBV, 76 proteins (HHBV-HHCC) among the HHBV (146) were also hepatocellular carcinoma-associated proteins (Figure 2B, Additional file 1, Table S6). Four HHBV-HHCC’s had more than 100 PMID references (Figure 2A). Gene ontology and KEGG pathway analysis The 146 HHBV could be classified into 18 mutually dependent functional sets, resulting in 17 cellular processes in 12 cellular components according to the gene ontology analysis. Accordingly, the 76 HHBV-HHCC could be classified into 14 functional sets, resulting in 16 cellular processes in eight cellular components (Additional file 1, Table S7). As shown in Figure 2C, most of the functional profiling showed transcriptional activity, DNA binding, kinase activity, signal transducer activity, cytokine activity and growth factor activity.

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