Computational Proteomics and Integration of Data Resources for Advanced Studies in Life Sciences

Editorial

23 July 2021

Editorial: Computational Proteomics and Integration of Data Resources for Advanced Studies in Life Sciences

Anna Marabotti

Paolo Romano

and

Angelo Facchiano

1,898 views

1 citations

Editors

Angelo Facchiano

Institute of Food Sciences, National Research Council (CNR)

Anna Marabotti

University of Salerno

Paolo Romano

San Martino Hospital (IRCCS)

Impact

Original Research

24 February 2021

Gene Set Enrichment Analysis of Interaction Networks Weighted by Node Centrality

Alessandra Zito

, 6 more and

Mauro Fasano

30,772 views

51 citations

Cell-type-specific and enteric nervous system (ENS) protein interactions. (A,B) Network maps representing the RRi and pathways regulated in microglia and oligodendrocytes. Note: red color denotes upregulation of a protein in the ENS. Triangle shape nodes indicate Parkinson’s disease (PD)-related proteins. Colored lines denote the interactions between the PD and ENS proteins. (C) The heatmap represents the PD proteins between the microglia and oligodendrocytes.

Original Research

25 September 2020

FGF2 Affects Parkinson’s Disease-Associated Molecular Networks Through Exosomal Rab8b/Rab31

Rohit Kumar

, 4 more and

Thomas Koeglsperger

5,241 views

19 citations

Samples dendrogram for Case Study 1 (ovarian cancer). On the left, the plot shows the overall dendrogram, where we enlighten two groups of samples in red rectangles. The red rectangle on the left is a cluster of samples from groups C to D. The red rectangle on the right (zoomed) represents a cluster of samples from groups A to B.

Technology and Code

29 March 2021

GeenaR: A Web Tool for Reproducible MALDI-TOF Analysis

Eugenio Del Prete

, 3 more and

Paolo Romano

10,278 views

9 citations

The studied system. (A) A schematic view represents briefly how classical and alternative complement pathways activated by antigen–antibody interaction, or by factors B and D, lead to C3 convertase production that eventually brings the MAC C5b–C9 components to assemble as a pore on the surface of the bacteria. (B,C) The bar graphs represent TIC-normalized intensity of complement proteins in human plasma adsorption samples. It provides a comparison between the wt strain SF370 (left) and the mutant strain ΔM1 (right) for C3 (B), C5, C6, C7, C8, and C9 components (C).

Original Research

08 January 2021

In vivo Cross-Linking MS of the Complement System MAC Assembled on Live Gram-Positive Bacteria

Hamed Khakzad

, 3 more and

Lars Malmström

3,169 views

10 citations

Gene interaction network (GIN) of AMPs characteristic of AD. The circles represent a gene/protein and the lines indicate interactions. The lines with arrow represent activation, blocking lines represent inhibition, simple lines represent protein–protein interaction. Line color indicates the type of interaction: green color refers to activation, red color to inhibition, blue color binding, whereas brown color shows co-expression. The red color of protein label indicates AMPs whose amount changed in a statistically significant manner between AD and control samples, the black color shows their interacting partners with no AMP activity, while the green color indicates interactors with AMP activity. On all panels the proteins are labeled with their gene name. The higher resolution images of the individual networks are presented in Supplementary Figure 5.

Original Research

28 April 2021

Construction of Unified Human Antimicrobial and Immunomodulatory Peptide Database and Examination of Antimicrobial and Immunomodulatory Peptides in Alzheimer’s Disease Using Network Analysis of Proteomics Datasets

Ajneesh Kumar

, 2 more and

Éva Csősz

2,963 views

10 citations

Original Research

03 December 2020

An Integrative Computational Approach Based on Expression Similarity Signatures to Identify Protein–Protein Interaction Networks in Female-Specific Cancers

Katia Pane

, 5 more and

Monica Franzese

3,205 views

6 citations

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