Graphic illustration of a functional modular map of the multiple gene/ protein analysis encompassing the candidate list of NAFLD and AFLD based on disease pathways.

<p>Results of functional association analysis performed by the bioinformatics resource <i>ToppCluster</i> (<a href="http://toppcluster.cchmc.org" target="_blank">http://toppcluster.cchmc.org</a>) based on pathways networks showing enriched terms from Gene Ontology, Mouse Phenotype, Co-expression, microRNAs, and transcription factors for the NAFLD- and AFLD-specific gene/protein lists. Right side of the figure depicts the highly significant enrichments for sets of genes and proteins of the NAFLD term list; left side of the figure depicts the highly significant enrichments for sets of genes and proteins of the AFLD term list; and the analysis of genes and intersection of pathways between NAFLD and AFLD is shown in the center part of the figure. Terms in red represent genes/proteins, and terms in green represent disease pathways in GO terms. The graph was constructed using the free available program Cytoscape, a software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058895#pone.0058895-Shannon1" target="_blank">[22]</a>.</p

Graphic illustration of genes/proteins co-occurrence and their relatedness to biological concepts with the query “alcoholic AND (steatosis OR fatty liver) NOT (non or nonalcoholic)”.

<p>Prediction was performed by PESCADOR (available at <a href="http://cbdm.mdc-berlin.de/tools/pescador/" target="_blank">http://cbdm.mdc-berlin.de/tools/pescador/</a>), a web-based tool to assist large-scale integration text-mining of biointeractions extracted from MEDLINE abstracts. The graph was constructed using the free available program MEDUSA, which is a Java application for visualizing and manipulating graphs of interaction (<a href="http://www.bork.embl.de/medusa" target="_blank">www.bork.embl.de/medusa</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058895#pone.0058895-Pavlopoulos1" target="_blank">[21]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058895#pone.0058895-Hooper1" target="_blank">[33]</a>.</p

Functional enrichment analysis of putative miRNAs associated with NAFLD and AFLD.

<p>The network is shown as a cytoscape graph <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058895#pone.0058895-Shannon1" target="_blank">[22]</a> generated from <i>ToppCluster</i> (available at toppcluster.cchmc.org/) network analysis.</p

Functional enrichment analysis of candidate genes and proteins previously associated with alcoholic liver disease (AFLD) and nonalcoholic fatty liver disease (NAFLD).

<p>The analysis was done by the bioinformatic resource <i>ToppGene Suite</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058895#pone-0058895-t001" target="_blank">Table 1</a> shows only top ranked and highly significant association. GO: gene ontology (<a href="http://www.geneontology.org/" target="_blank">http://www.geneontology.org/</a>).</p

Graphic illustration of genes/proteins co-occurrence and their relatedness to biological concepts with the query “nonalcoholic OR non-alcoholic AND fatty liver OR steatosis”.

<p>Prediction was performed by PESCADOR (available at <a href="http://cbdm.mdc-berlin.de/tools/pescador/" target="_blank">http://cbdm.mdc-berlin.de/tools/pescador/</a>), a web-based tool to assist large-scale integration text-mining of biointeractions extracted from MEDLINE abstracts. The graph was constructed using the free available program MEDUSA, which is a Java application for visualizing and manipulating graphs of interaction (<a href="http://www.bork.embl.de/medusa" target="_blank">www.bork.embl.de/medusa</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058895#pone.0058895-Pavlopoulos1" target="_blank">[21]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058895#pone.0058895-Hooper1" target="_blank">[33]</a>.</p

Comparative co-analysis of NAFLD and AFLD data sets focused on insulin signaling.

<p>Results of functional association analysis performed by the bioinformatics resource PESCADOR (available at <a href="http://cbdm.mdc-berlin.de/tools/pescador/" target="_blank">http://cbdm.mdc-berlin.de/tools/pescador/</a>), a web-based tool to assist large-scale integration text-mining of biointeractions extracted from MEDLINE abstracts with a focus in the selected terms. The graph was constructed using the free available program, MEDUSA, which is a Java application for visualizing and manipulating graphs of interaction (<a href="http://www.bork.embl.de/medusa" target="_blank">www.bork.embl.de/medusa</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058895#pone.0058895-Pavlopoulos1" target="_blank">[21]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058895#pone.0058895-Hooper1" target="_blank">[33]</a>. The thickness of the green lines signifies greater significance.</p

Analysis of interaction pathways (http://visant.bu.edu/) of SCD1; the metagraph structure allows the visualization of bionetworks constructed by integrative data-mining features, which permits a large number of functional associations for 103 different species.

<p>Direct SCD1-related nodes are shown in red. A few nodes are labeled for the sake of simplicity. The gene labels are official names.</p

Interventional experiment: Evaluation of the effect of clofibrate, an agonist of PPAR alpha, on hepatic Scd1 mRNA, protein expression and liver histology.

<div><p>Each bar represents the mean ± SE values of Sprague Dawley (SD) rats fed with standard chow diet CD (n=6), high fat diet HFD (n=5), and HFD plus clofibrate (n=5).</p> <p>In each sample, the gene expression was normalized to the expression of <i>Tbp</i> (TATA box binding protein). The arrow shows the characteristic hypertrophy of hepatocytes associated with PPAR alpha induction.</p> <p>The liver histology of a representative animal from each experimental group shows the hematoxylin-and-eosin staining of liver sections at the end of the experiment. Original magnification: 400×.</p></div

Left Panel: Liver histology of a representative animal from each experimental group.

<div><p>Hematoxylin and eosin staining of liver sections of a representative rat from each experimental group at the end of the experiment. The liver of rats fed with standard chow diet (CD) shows normal histology and absence of fat accumulation. The liver of rats fed with high fat diet (HFD) shows severe panlobular microvesicular and macrovesicular steatosis. Original magnification: 400×.</p> <p>Right panel: Phenotypic characteristics and biometric variables in the experimental models according to diet.</p> <p>Bar plots of steatosis score, liver triglyceride content, visceral fat weight (normalized by animal length), HOMA-IR, serum leptin levels (ng/mL), and body weight in Sprague Dawley (SD) rats that developed HFD-induced NAFLD without IR (upper panel) and in the HDF-induced NAFLD in the genetic model of MS in the SHR and its normotensive, insulin-sensitive control WKY strain (lower panel).</p> <p>HFD-induced NAFLD: Each bar represents the mean ± SE values of SD rats randomly divided into two experimental groups (CD: n=10; HFD: n=15).</p> <p>HFD-induced NAFLD in the genetic model of MS: Each bar represents the mean ± SE values of SHR (n=13) and WKY (n=14) randomly divided into two experimental groups (standard chow diet CD:SHR, n= 6 and WKY, n=7; high fat diet HFD: SHR, n=7 and WKY, n=7).</p></div

Analysis of liver <i>Scd1</i> mRNA abundance by quantitative real-time PCR in both experimental groups.

<div><p>Left panel: Each bar represents the mean ± SE values of Sprague Dawley (SD) rats randomly divided into two experimental groups (standard chow diet CD: n=10; high fat diet HFD: n=15).</p> <p>Right panel: Each bar represents the mean ± SE values of SHR (n=13) and WKY (n=14) divided into two experimental groups (CD:SHR, n= 6 and WKY, n=7; HFD: SHR, n=7 and WKY, n=7). The statistical significance of SHR vs. WKY indicates the comparison between strains independent of diet by two-way ANOVA.</p> <p>In each sample, the Scd1 expression was normalized by the expression of <i>Tbp</i> (TATA box binding protein).</p></div