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Methylation associated pathway activity deregulation in lung adenocarcinoma
CapSys - Systems Medicine of Community Acquired Pneumonia

Abstract (Expand)

Methylation impairments are tightly associated with gene expression and molecular pathway deregulation in cancer development. However, other regulatory mechanisms exist, making it important to distinguish … those from methylation driven changes. Here we specifically assessed molecular pathway states associated with gene methylation in lung adenocarcinoma. Paired gene expression and methylation data (id:GSE32867) were obtained from Gene Expression Omnibus. Self organizing maps (Wirth, H. et al.BMC Bioinformatics 2011;12:306 ) and in-house pathway signal flow algorithms were applied to describe expression (PSF) and methylation (mPSF) states in KEGG pathways. 35 and 24 KEGG pathways had at least one branch deregulated at significance levels p<0.05 and 0.05<p < 0.1, respectively. Because many pathways are multibranch, our analysis totalled in 54 up- (PSF>1) and 73 down-regulated (PSF<1) branches. From these branches, 19 were positively (mPSF<0) or negatively (mPSF>0) correlated with methylation states (see table).

Authors: L. Nersisyan, Henry Löffler-Wirth, A. Gevorgyan, Hans Binder, A. Arakelyan

Date Published: 2014

Publication Type: Not specified

Human Diseases: lung disease

Mining common pathway deregulation profiles in lung diseases
CapSys - Systems Medicine of Community Acquired Pneumonia

Abstract (Expand)

This study is aimed at investigating lung diseases described by common pathomechanisms based on evaluation of gene expression profiles in molecular pathways. 16 datasets containing 428 samples for 22 … health conditions were taken from Gene Expression Omnibus. Self organizing maps (Wirth, H. et al.BMC Bioinformatics 2011;12:306) and cluster analysis with dynamic tree cut were used for gene expression based disease clustering. In-house pathway signal flow algorithm and phylogenetic analysis were applied to find common pathway deregulation patterns in clusters. Analysis resulted in grouping the 22 conditions into 5 clusters (fig.1). PSF and phylogenetic analysis identified unique pathway deregulation patterns for each cluster (fig.2).

Authors: A. Arakelyan, L. Nersisyan, Henry Löffler-Wirth, Hans Binder

Date Published: 2014

Publication Type: Not specified

Human Diseases: lung disease

External ventricular drain infections: risk factors and outcome
SepNet - German Competence Network Sepsis

Abstract (Expand)

External ventricular drainage (EVD) is frequently used in neurosurgery to drain cerebrospinal fluid in patients with raised intracranial pressure. We performed a retrospective single center study in … order to evaluate the incidence of EVD-related infections and to identify underlying risk factors. 246 EVDs were placed in 218 patients over a 30-month period. EVD was continued in median for 7 days (range 1-44). The cumulative incidence of EVD-related infections was 8.3% (95% CI, 5.3-12.7) with a device-associated infection rate of 10.4 per 1000 drainage days (95% CI, 6.2-16.5). The pathogens most commonly identified were coagulase-negative Staphylococcus (62%) followed by Enterococcus spp. (19%). Patients with an EVD-related infection had a significantly longer ICU (11 versus 21 days, P \textless 0.01) and hospital stay (20 versus 28.5 days, P \textless 0.01) than patients without. Median total duration of external drainage was twice as long in patients with EVD-related infection (6 versus 12 days, P \textless 0.01). However, there was no significant difference in the duration between first EVD placement and the occurrence of EVD-related infection and EVD removal in patients without EVD-related infection (6 versus 7 days, P = 0.87), respectively. Interestingly no risk factor for EVD-related infection could be identified in our cohort of patients.

Authors: S. Hagel, T. Bruns, M. W. Pletz, C. Engel, R. Kalff, C. Ewald

Date Published: 2014

Publication Type: Journal article

Human Diseases: disease by infectious agent

Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs
Genetical Statistics and Systems Biology

Abstract (Expand)

BACKGROUND\backslashr\backslashnThe genome is pervasively transcribed but most transcripts do not code for proteins, constituting non-protein coding RNAs. Despite increasing numbers of functional reports … of individual long noncoding RNAs (lncRNAs), assessing the extent of functionality among the non-coding transcriptional output of mammalian cells remains intricate. In the protein coding world, transcripts differentially expressed in the context of processes essential for the survival of multicellular organisms have been instrumental for the discovery of functionally relevant proteins and their deregulation is frequently associated with diseases. We therefore systematically identify lncRNAs expressed differentially in response to oncologically relevant processes, cell-cycle, p53-, and STAT3 pathway, using tiling arrays.\backslashr\backslashnRESULTS\backslashr\backslashnWe find that up to 80% of the pathway-triggered transcriptional response can be non-coding. Among these we identify very large macroRNAs with pathway-specific expression patterns and demonstrate that these are likely continuous transcripts. MacroRNAs contain elements conserved in mammals and sauropsids, which in part exhibit conserved RNA secondary structure. Comparing evolutionary rates of a macroRNA to adjacent protein coding genes suggests a local action of the transcript. Finally, in different grades of astrocytoma, a tumor disease unrelated to the initially used cell lines, macroRNAs are differentially expressed.\backslashr\backslashnCONCLUSIONS\backslashr\backslashnIt has been shown previously that the majority of expressed non-ribosomal transcripts are non-coding. We now conclude that differential expression triggered by signaling pathways gives rise to a similar abundance of non-coding content. It is thus unlikely that the prevalence of non-coding transcripts in the cell is a trivial consequence of leaky or random transcription events. BACKGROUND The genome is pervasively transcribed but most transcripts do not code for proteins, constituting non-protein-coding RNAs. Despite increasing numbers of functional reports of individual long non-coding RNAs (lncRNAs), assessing the extent of functionality among the non-coding transcriptional output of mammalian cells remains intricate. In the protein-coding world, transcripts differentially expressed in the context of processes essential for the survival of multicellular organisms have been instrumental in the discovery of functionally relevant proteins and their deregulation is frequently associated with diseases. We therefore systematically identified lncRNAs expressed differentially in response to oncologically relevant processes and cell-cycle, p53 and STAT3 pathways, using tiling arrays. RESULTS We found that up to 80% of the pathway-triggered transcriptional responses are non-coding. Among these we identified very large macroRNAs with pathway-specific expression patterns and demonstrated that these are likely continuous transcripts. MacroRNAs contain elements conserved in mammals and sauropsids, which in part exhibit conserved RNA secondary structure. Comparing evolutionary rates of a macroRNA to adjacent protein-coding genes suggests a local action of the transcript. Finally, in different grades of astrocytoma, a tumor disease unrelated to the initially used cell lines, macroRNAs are differentially expressed. CONCLUSIONS It has been shown previously that the majority of expressed non-ribosomal transcripts are non-coding. We now conclude that differential expression triggered by signaling pathways gives rise to a similar abundance of non-coding content. It is thus unlikely that the prevalence of non-coding transcripts in the cell is a trivial consequence of leaky or random transcription events.

Authors: Jörg Hackermüller, Kristin Reiche, Christian Otto, Nadine Hösler, Conny Blumert, Katja Brocke-Heidrich, Levin Böhlig, Anne Nitsche, Katharina Kasack, Peter Ahnert, Wolfgang Krupp, Kurt Engeland, Peter F. Stadler, Friedemann Horn

Date Published: 2014

Publication Type: Journal article

Anforderungen an ein modernes und umfassendes Informationsmanagement für Krankenhäuser
Management of health information systems

Abstract

Not specified

Author: Alfred Winter

Date Published: 2014

Publication Type: InCollection

How to Assess Quality of Electronic Health Record Systems
Management of health information systems

Abstract

Not specified

Author: Alfred Winter

Date Published: 2014

Publication Type: InCollection

Customer-enabled orchestration of complex services: A new paradigm even for health care?
Management of health information systems

Abstract

Not specified

Authors: Alfred Winter, R. Alt, Jan Ehmke, Reinhold Haux, Dirk Mattfeld, A. Oberweis, Barbara Paech

Date Published: 2014

Publication Type: Journal article

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