PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

Mi, Huaiyu; Guo, Nan; Kejariwal, Anish

doi:10.1093/nar/gkl869

Cited by 344 publications

(290 citation statements)

References 20 publications

Supporting

Mentioning

287

Contrasting

Unclassified

Order By: Relevance

“…Differentially expressed proteins (DEPs) were classified based on the PANTHER (Protein ANalysis THrough Evolutionary Relationships) system (http://www.pantherdb.org), which classifies genes and proteins by their functions. 35 A DEP interaction network was generated with Pathway Studio version 5.0 (Ariadne Genomis, Rockville, MD) and the Resnet 5 database. 36 Common downstream targets or upstream regulators of multiple proteins were identified using this software, which facilitated the process of selecting key factors and potential mechanisms from the large number of proteins.…”

Section: Methodsmentioning

confidence: 99%

Quantitative Proteomic Analysis of Tumor Reversion in Multiple Myeloma Cells

Zhang

Tao

et al. 2010

J. Proteome Res.

View full text Add to dashboard Cite

Tumor reversion is defined as the process by which cancer cells lose their malignant phenotype. However, relatively little is known about the cellular proteome changes that occur during the reversion process. A biological model of multiple myeloma (MM) reversion was established by using the H-1 parvovirus as a tool to select for revertant cells from MM cells. Isolated revertant cells displayed a strongly suppressed malignant phenotype both in vitro and in vivo. To explore possible mechanisms of MM reversion, the protein profiles of the revertant and parental MM cells were compared using a quantitative proteomic strategy termed SILAC-MS. Our results revealed that 379 proteins were either activated or inhibited during the reversion process, with a much greater proportion of the proteins, including STAT3, TCTP, CDC2, BAG2, and PCNA, being inhibited. Of these, STAT3, which is significantly down regulated, was selected for further functional studies. Inhibition of STAT3 expression by RNA interference resulted in suppression of the malignant phenotype and concomitant down regulation of TCTP expression, suggesting that myeloma reversion operates, at least in part, through inhibition of STAT3. Our results provide novel insights into the mechanisms of tumor reversion and suggest new alternative approaches for MM treatment.

show abstract

Section: Methodsmentioning

confidence: 99%

Quantitative Proteomic Analysis of Tumor Reversion in Multiple Myeloma Cells

Zhang

Tao

et al. 2010

J. Proteome Res.

View full text Add to dashboard Cite

show abstract

“…26 Some proteins were annotated manually based on literature searches and closely related homologues.…”

Section: Bioinformatic Analysismentioning

confidence: 99%

Identification of Novel miR-21 Target Proteins in Multiple Myeloma Cells by Quantitative Proteomics

et al. 2012

View full text Add to dashboard Cite

Substantial evidence indicates that microRNA-21 (miR-21) is a key oncomiR in carcinogenesis and is significantly elevated in multiple myeloma (MM). In this study, we explored the role of miR-21 in human MM cells and searched for miR-21 targets. By knocking down the expression of endogenous miR-21 in U266 myeloma cells, we observed reduced growth, an arrested cell cycle, and increased apoptosis. To further understand its molecular mechanism in the pathogenesis of MM, we employed a SILAC (stable isotope labeling by amino acids in cell culture)-based quantitative proteomic strategy to systematically identify potential targets of miR-21. In total, we found that the expression of 178 proteins was up-regulated significantly by miR-21 inhibition, implying that they could be potential targets of miR-21. Among these, the protein inhibitor of activated STAT3 (PIAS3) was confirmed as a direct miR-21 target by Western blotting and reporter gene assays. We further demonstrated that miR-21 enhances the STAT3-dependent signal pathway by inhibiting the function of PIAS3 and that down-regulation of PIAS3 contributes to the oncogenic function of miR-21. This elucidation of the role of PIAS3 in the miR-21-STAT3 positive regulatory loop not only may shed light on the molecular basis of the biological effects of miR-21 observed in MM cells but also has direct implications for the development of novel anti-MM therapeutic strategies.

show abstract

“…We furthermore searched for biological pathways enriched/depleted in DEGs using the PANTHER (Protein Analysis Through Evolutionary Relationships) Classification System. 21 …”

Section: Statistical and Pathway Analysismentioning

confidence: 99%