ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data

Antonov, Alexey V.; Schmidt, Thorsten; Wang, Yu; Mewes, Hans‐Werner

doi:10.1093/nar/gkn239

Cited by 70 publications

(72 citation statements)

References 33 publications

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“…Primary and secondary patency 12 months after revascularization was 39% and 53%, respectively; there were no amputations or death events. In our cohort, primary revascularization success was observed in the vast majority of all cases (>98%), which was comparable to the results of previous trials 12,18,19. Generally, our collective of 202 patients was characterized by a substantial heterogeneity.…”

Section: Discussionsupporting

confidence: 87%

A comparative study on endovascular treatment of (sub)acute critical limb ischemia: mechanical thrombectomy vs thrombolysis

Kronlage¹,

Printz²,

Vogel³

et al. 2017

DDDT

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ObjectiveThe aim of this study was to compare different interventional methods for treatment of (sub)acute limb ischemia upon thrombotic occlusions of the lower extremity in terms of their safety and efficacy in a tertiary hospital setting.DesignThis is a retrospective, single-center study of non-randomized data.MethodsA total of 202 patients, including 26 critically ill patients, underwent rotational thrombectomy (Rotarex®), local thrombolysis (recombinant tissue plasminogen activator), or combination of both at the University Hospital Heidelberg (2006–2015). The different interventional procedures were compared in terms of overall and amputation-free survival, as well as patency in a 1-year follow-up (Kaplan–Meier analysis).ResultsThe study demonstrated a primary revascularization success of >98% in all groups. One year after revascularization, primary and secondary patency after mechanical thrombectomy alone were significantly better in comparison to local thrombolysis or a combination of Rotarex® and lysis (63% and 85%, P<0.05). Overall survival 12 months after intervention reached up to 96% in noncritically ill patients, and amputation-free survival was 94.3% in all three groups. Mean hospitalization duration and rate of major bleedings were significantly increased after thrombolysis compared to Rotarex® (P<0.05).ConclusionIn patients with (sub)acute limb ischemia, Rotarex® mechanical thrombectomy represents a safe and effective alternative to thrombolysis and is associated with a reduced rate of major bleedings, shorter hospitalization durations, and lower costs.

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Section: Discussionsupporting

confidence: 87%

A comparative study on endovascular treatment of (sub)acute critical limb ischemia: mechanical thrombectomy vs thrombolysis

Kronlage¹,

Printz²,

Vogel³

et al. 2017

DDDT

View full text Add to dashboard Cite

show abstract

“…Criteria for pathway enrichment were: (1) significance of association between the canonical pathway and the dataset (p<0.05, Fischer's exact test); and (2) degree of enrichment (>1% unique genes from the input dataset belonging to the pathway). Functional categories enriched in the gene datasets were determined by Gene Ontology (GO) analysis using GeneSpring software and ProfCom analytic tool [67]. For selected gene sets, Spearman's rank correlation coefficient (Rho) was determined using StatView (SAS Institute Inc, Cary, NC).…”

Section: Methodsmentioning

confidence: 99%

Cigarette smoking reprograms apical junctional complex molecular architecture in the human airway epithelium in vivo

Shaykhiev

Otaki

Bonsu

et al. 2010

Cell. Mol. Life Sci.

191

202

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Summary The apical junctional complex (AJC), composed of tight and adherens junctions, maintains epithelial barrier function. Since cigarette smoking and chronic obstructive pulmonary disease (COPD), the major smoking-induced disease, are associated with increased lung epithelial permeability, we hypothesized that smoking alters the transcriptional program regulating airway epithelial AJC integrity. Transcriptome analysis revealed global down-regulation of physiological AJC gene expression in the airway epithelium of healthy smokers (n=59) compared to nonsmokers (n=53) in association with changes in canonical epithelial differentiation pathways such as PTEN signaling accompanied by induction of cancer-related AJC components. The overall expression of AJC-related genes was further decreased in COPD smokers (n=23). Exposure of airway epithelial cells to cigarette smoke extract in vitro resulted in down-regulation of several AJC genes paralleled by decreased transepithelial resistance. Thus, cigarette smoking induces transcriptional reprogramming of airway epithelial AJC architecture from its physiological pattern necessary for barrier function toward disease-associated molecular phenotype.

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“…Integrative data analysis, including multiple graphical visualizations, was performed using GenespringGX10 (Agilent Biotechnologies) and pathway analysis by the Kyoto Encyclopedia of Genes and Genomes (KEGG). The profile of functional pathways was analyzed using ProfCom software (21). This software allows comparing the proportion of genes related to specific gene ontology categories (biological process, cellular component, and molecular function) among the ATM higher expressed genes to the proportion of genes related to the same category within the gene ontology reference set of all genes from Homo sapiens (21).…”

Section: ϫ5mentioning

confidence: 99%

Human Adipose Tissue Macrophages Display Activation of Cancer-related Pathways

Mayi

Daoudi

Derudas

et al. 2012

Journal of Biological Chemistry

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ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data

Cited by 70 publications

References 33 publications

A comparative study on endovascular treatment of (sub)acute critical limb ischemia: mechanical thrombectomy vs thrombolysis

A comparative study on endovascular treatment of (sub)acute critical limb ischemia: mechanical thrombectomy vs thrombolysis

Cigarette smoking reprograms apical junctional complex molecular architecture in the human airway epithelium in vivo

Human Adipose Tissue Macrophages Display Activation of Cancer-related Pathways

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