PetriScape - A plugin for discrete Petri net simulations in Cytoscape

Almeida, Diogo Rafael Silva De; Azevedo, Vasco; Silva, Artur M. S.; Baumbach, Jan

doi:10.2390/biecoll-jib-2016-284

Cited by 4 publications

(1 citation statement)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To examine the connections among the target genes, a protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes database (STRING version 11.5, http: //stringdb.org) 15 . Cytoscape (version 3.7.2) software was used for the visualization of the PPI network 16 .…”

Section: Construction Of Protein-protein Interaction Networkmentioning

confidence: 99%

In silico and in vitro analysis of differentially expressed microRNAs, circular RNAs, and p53 in bortezomib-resistant multiple myeloma

2022

View full text Add to dashboard Cite

Background: Multiple myeloma (MM), which constitutes 1% of all cancers, remains incurable due to the acquisition of drug resistance. Proteasome inhibitor therapy such as bortezomib (BTZ), one of the key therapies used to treat MM, is impeded by the occurrence of BTZ resistance. The precise mechanism underlying this acquired BTZ resistance in MM is not yet well understood. In recent times, the role of non-coding RNAs, such as microRNAs (miRNAs) and circular RNAs (circRNAs), in cancer progression and drug resistance has been demonstrated. The present study aimed to identify differentially expressed miRNAs (DEmiRs), circRNAs, and target genes in BTZ-resistant MM in silico and in vitro. Methods: DEmiRs were obtained and analyzed from microarray datasets of MM patients from the Gene Expression Omnibus (GEO) database using GEO2R. Targets of a DEmiR were detected using mirDIP software. Gene ontology and pathway enrichment analysis of the targets were executed using the DAVID database. A protein-protein interaction network of targets was constructed and analyzed using the STRING database and Cytoscape tool. Expression levels of a DEmiR and an interacting circRNA were assessed by qRT-PCR. Target gene expression was assessed by qRT-PCR and western blot. Results: Among the identified DEmiRs, hsa-mir-151a-3p was found to be upregulated in BTZ-resistant MM. One circRNA, hsa_circ_0000073, that was predicted to interact with hsa-mir-151a-3p using the CircInteractome platform, was downregulated in BTZ-resistant MM. Among the targets of hsa-mir-151a-3p, p53 was downregulated at both the transcript and protein levels in BTZ-resistant MM. Conclusions: This study indicates that these molecular players could be implicated in BTZ-resistant MM.

show abstract

Section: Construction Of Protein-protein Interaction Networkmentioning

confidence: 99%

In silico and in vitro analysis of differentially expressed microRNAs, circular RNAs, and p53 in bortezomib-resistant multiple myeloma

2022

View full text Add to dashboard Cite

show abstract

Identification BCL6 and miR-30 family associating with Ibrutinib resistance in activated B-cell-like diffuse large B-cell lymphoma

Huang

Zhang

et al. 2021

Med Oncol

View full text Add to dashboard Cite

Ibrutinib has clear efficacy for activated B-cell-like diffuse large B cell lymphoma (ABC-DLBCL) in previous clinical researches. However, the resistance of Ibrutinib has limited its therapeutic benefit and the potential mechanism remains unclear. This study was aimed to identify potential candidate genes and miRNA targets to overcome Ibrutinib resistance in ABC-DLBCL. First, two expression profiles were downloaded from the GEO database, which used to identify the DEGs related to Ibrutinib resistance in ABC-DLBCL cell lines by GEO2R analysis separately. And the common DEGs were obtained though Venn diagram. Then Gene ontology (GO) and pathway enrichment analysis were conducted by DAVID database. From STRING database, BCL6, IL10, IL2RB, IRF4, CD80, PRDM1and GZMB were determined to be the hub genes by protein–protein interaction (PPI) network. Through miRNA-mRNA targeting network, we found that BCL6, IRF4, CD80, and PRDM1 were common target genes of miR-30 family. The cBioPortal database showed that BCL6 had the highest level of genetic alterations among DLBCL. In addition, another expression profile from GEO database showed that BCL6 was significantly high expression in no responsive patients after Ibrutinib treatment, and the receiver operating characteristic (ROC) curve which was used to evaluate the relationship between BCL6 expression and its effect was 0.67. MTT assay showed that treatment with FX1 (a BCL6 inhibitor) can enhance the sensitivity of Ibrutinib in C481S BTK HBL-1 cells. The results suggested that BCL6 and miR-30 family maybe associate with Ibrutinib resistance in ABC-DLBCL.

show abstract

In silico bioinformatics analysis for identification of differentially expressed genes and therapeutic drug molecules in Glucocorticoid-resistant Multiple myeloma

Ghosal

Banerjee

2022

Med Oncol

View full text Add to dashboard Cite

PetriScape - A plugin for discrete Petri net simulations in Cytoscape

Cited by 4 publications

References 15 publications

In silico and in vitro analysis of differentially expressed microRNAs, circular RNAs, and p53 in bortezomib-resistant multiple myeloma

In silico and in vitro analysis of differentially expressed microRNAs, circular RNAs, and p53 in bortezomib-resistant multiple myeloma

Identification BCL6 and miR-30 family associating with Ibrutinib resistance in activated B-cell-like diffuse large B-cell lymphoma

In silico bioinformatics analysis for identification of differentially expressed genes and therapeutic drug molecules in Glucocorticoid-resistant Multiple myeloma

Contact Info

Product

Resources

About