The comprehensive rankings of all thirteen candidate reference genes.

<p>The comprehensive rankings of all thirteen candidate reference genes.</p

Distribution of threshold cycle (Ct) values for candidate reference genes obtained using qPCR in <i>C. elegans</i>.

<p>Boxes show the range of Ct values within each candidate gene; the black centre line indicates the median Ct; the extended upper and lower hinges indicate 75 and 25 percentiles; the whiskers show the largest/smallest Ct values that falls within a distance of 1.5 times IQR (Interquartile range) from the upper and lower hinges; outliers are shown as small circles.</p

Expression stability evaluated by BestKeeper.

<p>Expression stability evaluated by BestKeeper.</p

Additional file 1 of Repurposing a clinically approved prescription Colquhounia root tablet to treat diabetic kidney disease via suppressing PI3K/AKT/NF-kB activation

Additional file 1: Table S1. Includes detailed information of all enzyme-linked immunosorbent assay kits. Table S2. Includes 672 putative target genes of CRT predicted using ETCM database and TCMIP v2.0 platform. Table S3. Includes 3472 DKD-related genes from Human Phenotype Ontology (HPO), DisGeNet and Drugbank databases. Table S4. Includes enrichment results of clinical symptoms of 390 CRT putative targets. Table S5. Includes enrichment results of functional modules of 390 CRT putative targets. Table S6. Includes 231 candidate targets of CRT against DKD in “Disease Gene-Drug Target” interaction networks based on calculated network topological features. Table S7. Includes enrichment results of functional modules of 231 CRT candidate targets

The average expression stability values of the thirteen candidate reference genes analyzed by geNorm.

<p>The lower the M value, the higher the stability.</p

Primer amplification efficiency of the thirteen candidate reference genes.

<p>Primer amplification efficiency of the thirteen candidate reference genes.</p

Determination of the optimal number of reference genes by geNorm analysis of the pairwise variation (V_n/n+1).

<p>Determination of the optimal number of reference genes by geNorm analysis of the pairwise variation (V_n/n+1).</p

Primer Information of Selected Candidate Reference Genes.

<p>Primer Information of Selected Candidate Reference Genes.</p

Identification of GRB2 and GAB1 Coexpression as an Unfavorable Prognostic Factor for Hepatocellular Carcinoma by a Combination of Expression Profile and Network Analysis

<div><p>Aim</p><p>To screen novel markers for hepatocellular carcinoma (HCC) by a combination of expression profile, interaction network analysis and clinical validation.</p> <p>Methods</p><p>HCC significant molecules which are differentially expressed or had genetic variations in HCC tissues were obtained from five existing HCC related databases (OncoDB.HCC, <a href="http://hcc.net" target="_blank">HCC.net</a>, dbHCCvar, EHCO and Liverome). Then, the protein-protein interaction (PPI) network of these molecules was constructed. Three topological features of the network ('Degree', 'Betweenness', and 'Closeness') and the k-core algorithm were used to screen candidate HCC markers which play crucial roles in tumorigenesis of HCC. Furthermore, the clinical significance of two candidate HCC markers growth factor receptor-bound 2 (GRB2) and GRB2-associated-binding protein 1 (GAB1) was validated.</p> <p>Results</p><p>In total, 6179 HCC significant genes and 977 HCC significant proteins were collected from existing HCC related databases. After network analysis, 331 candidate HCC markers were identified. Especially, GAB1 has the highest k-coreness suggesting its central localization in HCC related network, and the interaction between GRB2 and GAB1 has the largest edge-betweenness implying it may be biologically important to the function of HCC related network. As the results of clinical validation, the expression levels of both GRB2 and GAB1 proteins were significantly higher in HCC tissues than those in their adjacent nonneoplastic tissues. More importantly, the combined GRB2 and GAB1 protein expression was significantly associated with aggressive tumor progression and poor prognosis in patients with HCC.</p> <p>Conclusion</p><p>This study provided an integrative analysis by combining expression profile and interaction network analysis to identify a list of biologically significant HCC related markers and pathways. Further experimental validation indicated that the aberrant expression of GRB2 and GAB1 proteins may be strongly related to tumor progression and prognosis in patients with HCC. The overexpression of GRB2 in combination with upregulation of GAB1 may be an unfavorable prognostic factor for HCC.</p> </div

MOESM2 of A novel gene-expression-signature-based model for prediction of response to Tripterysium glycosides tablet for rheumatoid arthritis patients

Additional file 2. Primer sequences used in the qPCR analysis