Additional file 3 of SynBioTools: a one-stop facility for searching and selecting synthetic biology tools

Additional file 3. The list of reviews used for the tool and tool information extraction

Additional file 2 of SynBioTools: a one-stop facility for searching and selecting synthetic biology tools

Additional file 2. The code zip file on extracting tabular information from papers by paring the full-text XML file

Additional file 1 of SynBioTools: a one-stop facility for searching and selecting synthetic biology tools

Additional file 1. The code zip file on extracting tabular information from papers in PDF format based on OCR

Validation of differentially expressed proteins by immunoblot analysis.

<p>Validation of differentially expressed proteins by immunoblot analysis.</p

Quantitative Proteomic Profiling the Molecular Signatures of Annexin A5 in Lung Squamous Carcinoma Cells

<div><p>Lung cancer remains the leading cancer killer around the world. It’s crucial to identify newer mechanism-based targets to effectively manage lung cancer. Annexin A5 (ANXA5) is a protein kinase C inhibitory protein and calcium dependent phospholipid-binding protein, which may act as an endogenous regulator of various pathophysiological processes. However, its molecular mechanism in lung cancer remains poorly understood. This study was designed to determine the mechanism of ANXA5 in lung cancer with a hope to obtain useful information to provide a new therapeutic target. We used a stable isotope dimethyl labeling based quantitative proteomic method to identify differentially expressed proteins in NSCLC cell lines after ANXA5 transfection. Out of 314 proteins, we identified 26 and 44 proteins that were down- and up-regulated upon ANXA5 modulation, respectively. The IPA analysis revealed that glycolysis and gluconeogenesis were the predominant pathways modulated by ANXA5. Multiple central nodes, namely HSPA5, FN1, PDIA6, ENO1, ALDOA, JUP and KRT6A appeared to occupy regulatory nodes in the protein-protein networks upon ANXA5 modulation. Taken together, ANXA5 appears to have pleotropic effects, as it modulates multiple key signaling pathways, supporting the potential usefulness of ANXA5 as a potential target in lung cancer. This study might provide a new insight into the mechanism of ANXA5 in lung cancer.</p></div

ALDOA is highly expressed in lung squamous carcinoma.

<p>(A) Proteomic analysis of the differentially expressed proteins from normal tissue and LSCC metastasis. Strictly selected 7 pairs of the matched LSCC specimens were subjected for 2D-DIGE and MS proteomic analysis. ALDOA was up-regulated 3.12-fold in metastatic LSCC tissues and 1.77-fold in non-metastatic LSCC tissues compared to adjacent normal tissues (the pointing arrow shows the ALDOA spots). (B) The amino acid residues highlighted in red were those detected by MS/MS analysis and counted for 36% sequence coverage of ALDOA. (C) Western blotting analysis of the ALDOA protein expression in 17 pairs of LSCC and matched adjacent normal tissues. Higher expression of ALDOA was observed in most of LSCC tissues examined. Data from 6 pairs of specimens were shown here. (D) Average of the ALDOA protein from 17 pairs of matched specimens. The relative expression values of ALDOA were 0.87±0.47 in carcinoma tissues and 0.54±0.27 in normal tissues. The level of Actin was used as control for normalization.</p

Summary of the TMA analysis of ALDOA expression.

<p>Correlations of the protein level of ALDOA in LSSC tissues and tumor metastasis, grade and differentiation status. Of the total 75 specimens on TMA examined, 32 pairs are from metastatic LSCC patients and 43 pairs are from non-metastatic LSCC patients. The intensity of the positive stain of TMA was measured and quantified as positive (+) or strong positive (++).</p

The expression level of ANXA5 in LUSC and LUAD patients.

<p>The expression level of ANXA5 in LUSC and LUAD patients.</p

Expression level of ALDOA protein is negatively correlated with survival rates and prognosis of LSCC patients.

<p>Thirty-two out of the 75 cases on TMA met the requirement for the Kaplan-Meier method analysis. −: negative expression; +: positive expression; ++: strong positive expression.</p

ALDOA is a major cytoplasmic protein.

<p>(<b>A</b>) Endogenous ALDOA was detected by immunofluorescence staining using antibody specific to ALDOA in NCI-H520 cells. Cellular ALDOA protein (red) and nuclear condensation (blue, DAPI) were examined by using a Leica confocal SP5 microscopey. (B) IHC assays of ALDOA were performed in paired LSCC tissues vs adjacent normal tissues.</p