geneXplain-platform

geneXplain platform

The comprehensive bioinformatics platform, also available as Java API

Major platform release 5.0 is out now !

 

The geneXplain platform is an online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system.With this system, you can edit the predefined workflows or compose your own workflows from scratch.

Own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses.

GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field.

geneXplain start page

The start page provides an easy access to a number of application areas. Click image for full picture.

Key features

Integrated databases and analysis tools

The platform provides an integrated view on several databases and analysis tools, public domain as well as commercial ones. They can be combined in a highly flexible way to design customized analyses.

Ready-made workflows for an easy start

A rapidly growing number of proven workflows facilitates a quick and easy access to the platform and its complex analysis functions. Input forms are simple and user-friendly. Workflows can be easily customized to specific needs. Experienced users can create their own workflows.

Fully integrated upstream analysis

The platform provides a fully integrated upstream analysis, which combines state-of-the-art analysis of regulatory genome regions with sophisticated pathway analyses.

Knowledge-based data analysis

The platform uses a number of renowned high-quality databases for the data analysis. TRANSFAC® and TRANSPATH® are expert-curated databases. GeneWays is generated by an NLP-based text-mining approach, providing a helpful complement for manually curated data. Well-known public-domain databases like Reactome and HumanCyc are integrated and applied as well.

JavaScript and R scripts

User-specific scripts in JavaScript and in R can be added directly into the platform, and immediately executed. They can be combined with pre-existing analyses, and can be part of the workflows.

NGS data analysis

NGS data analysis is supported by the platform. ChIP-seq data sets containing in vivo transcription factor binding sites or methylation results can be analyzed with the help of ready-made workflows. Galaxy tools are integrated, supporting RNA-seq data analysis, and many functions more.

Simulation engine inside

The platform contains a simulation engine that executes differential equation systems and visualizes the results. Parameter optimization, parameter fitting (based on expression data), and hierarchical modeling are supported.

Group project work including chat function

Share your data and results with other members of the project. Discuss what you are doing while working together on a dataset.

Major features

New workflows

  • A new set of workflows is summarized under the start page button Metabolism
  • Flux balance analysis to identify enzymes, reactions and metabolites including clustering and mapping of flux data
  • Enriched upstream analysis (TRANSFAC® and TRANSPATH®)
  • Focused upstream analysis (TRANSFAC® and TRANSPATH®)
  • Upstream analysis with feedback loop (TRANSFAC® and TRANSPATH®) indicates master regulators with expression values (fold changes) from the input set
  • Identify enriched motifs in tissue specific tracks (TRANSFAC®)
  • Cross-species identification of enriched motifs in promoters
  • Cross-species mapping to ontologies

New and updated databases

  • Human Metabolic Reaction (HMR): HMR2 contains 3.765 genes associated with over 8.000 reactions and over 3.000 unique metabolites.
  • Human metabolism global reconstruction (Recon 2): The most comprehensive representation of human metabolism that is applicable to computational modeling
  • Integration of the latest TRANSFAC® and TRANSPATH® versions (releases 2016.2)
  • HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO): This database provides transcription factor (TF) binding models for 601 human and 396 mouse TFs, partially based on TRANSFAC.
  • Reactome database has been updated to version 57.
  • GO (Gene Ontology Database) has been updated to version 06.2015.
  • Integration of new Ensembl versions (release 84), Ensembl Homo sapiens (hg38), Ensembl Mus musculus (mm10), Ensembl Rattus norvegicus (rn6)

New methods

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Remove overlapping sites
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Preprocess raw reads
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Site search report
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Convert site search summary
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Find longest connected chains
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Match genes and metabolites
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Building flux balance data table
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Flux balance constraint
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Score based FBC table builder
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Heatmap
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Variance filter

New release

RELEASE 5.0

Download full feature list

  • Database update:

Ensembl version is updated to Ensembl release 96 (April 2019).

  • New RNA-seq features:

Rsubread – a Bioconductor software package that provides high-performance alignment and read
counting functions for RNA-seq reads (NAR February 2019). Rsubread integrates read mapping and
quantification in a single package.

Subread-align

Subread is a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq
reads, based on its unique seed-and-vote design, by which a large number of 16mer subreads
from each read are mapped to the reference genome. The subread function accepts raw reads
in the form of Fastq, SAM or BAM files and output read alignments in either SAM or BAM
format. The output contains the total number of reads, the number of uniquely mapped reads,
the number of multi-mapping reads and other mapping statistics. The align function is
exceptionally flexible. It performs local read alignment and reports the largest mappable region
for each read.
The align function automatically detects insertions and deletions (indels). First step of indels
identification is mapping 16mer subreads from each read to the genome and determination of
the major mapping location of the read. The second step undertakes a detailed local realignment of each read with the aid of collected indels. The align function also writes VCF files
containing detected indels.
The align function can align read pairs arbitrarily far apart if the alignment is sufficiently good
and no more canonical alignment is available. A weighting strategy is used to give preference
to alignments within the expected fragment length bounds. Gene fusions are now supported
by allowing different subreads from the same read to map to different chromosomes.

Subjunc

Subjunc is an RNA-seq read aligner that provides comprehensive detection of exon–exon junctions and reports full alignments of junction-spanning reads in BED file format.
First part is mapping a large number of 16mer subreads from each read to the genome. This
step detects exon–exon junctions and determines the major mapping location of the read. The
second part undertakes a detailed local re-alignment of each read with the aid of collected
junctions.
Subjunc function can detect exon–exon junctions de novo and to quantify expression at the
level of either genes, exons or exon junctions.

featureCounts

The featureCounts function counts the number of reads or read-pairs that overlap any specified set
of genomic features. It can assign reads to any type of genomic region. Regions may be specified as
simple genomic intervals (promoter regions) or can be collections of genomic intervals (genes
comprising multiple exons). Any set of genomic features can be specified in GTF, GFF or SAF file
format. SAF is a Simplified Annotation Format with columns GeneID, Chr, Start, End and Strand.

FeatureCounts produces a matrix of gene-wise counts and can be used as input for gene
expression analysis with limma, edgeR or DESeq2. Alternatively, a matrix of exon-level counts
can be produced suitable for differential exon usage analyses using limma, edgeR or DEXSeq.
FeatureCounts outputs the genomic length and position of each feature as well as the read
count, making it straightforward to calculate summary measures such as RPKM (reads per
kilobase per million reads).

exactSNP

The exactSNP function calls SNPs for individual samples, without requiring control samples to
be provided. It tests the statistical significance of SNPs by comparing SNP signals to their
background noises.

Limma-Voom

The Limma-voom function performs differential expression analysis for pre-processed RNA-seq
data (single channel experiments) with sample-specific quality weights when the library sizes
are quite variable between samples or the presence of outlier samples is given. The output
reports the top100 differentially expressed genes and a pdf document containing density plots
from raw and filtered counts, plot about the Mean−variance trend and gives visual information
about sample clustering.

Guided linear model analysis

GeneXplain’s in-house implementation of a linear model analysis using Limma with experimental
design specified through an annotation table. This tool performs linear model analysis on the given
input table guided by selected experimental factors defined in a sample table. The analysis aims at
finding significant differences between pairs of levels of a main factor. Furthermore, an ANOVA is
carried out for all contrasts together. The assignment of main factor levels to columns of the input
table is specified in a column of a sample table. Additional variables can be controlled by providing
their column names in the sample table. Moreover, Surrogate Variable Analysis can be included to
infer unspecified factors.

HISAT2

HISAT is a very fast and sensitive alignment tool for mapping next-generation sequencing reads (DNA and RNA) to a population of human genomes (as well as to a single reference genome). HISAT2 uses
a large set of small GFM indexes that collectively cover the whole genome (each index representing
a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These
small indexes (called local indexes), combined with several alignment strategies, enable rapid and
accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph
FM index (HGFM).
HISAT provides several alignment strategies specifically designed for mapping different types of
RNA-seq reads. All these together, HISAT enables extremely fast and sensitive alignment of reads,
in particular those spanning two exons or more. As a result, HISAT is much faster (over 50 times)
than TopHat2 with better alignment quality. HISAT uses the Bowtie2 implementation to handle
most of the operations on the FM index. In addition to spliced alignment, HISAT handles reads
involving indels and supports a paired-end alignment mode. HISAT outputs alignments in SAM
format.

HTseq-count

This tool takes an alignment file in SAM or BAM format and feature file in GFF format and calculates
the number of reads mapping to each feature. It uses the htseq-count script that is part of the HTSeq
python module.
A feature is an interval (i.e., a range of positions) on a chromosome or a union of such intervals. In
the case of RNA-Seq, the features are typically genes, where each gene is considered here as the
union of all its exons. One may also consider each exon as a feature, e.g., in order to check for
alternative splicing. For comparative ChIP-Seq, the features might be binding regions from a predetermined list.

HTseq-qa

This tool takes a file with high-throughput sequencing reads (either raw or aligned reads) and
performs a simple quality assessment by producing plots showing the distribution of called bases
and base-call quality scores by position within the reads. Output is a PDF file with all quality plots.

Empirical Analysis of Digital Gene Expression Data in R (EdgeR)

Differential expression analysis of RNA-seq expression profiles with biological replication.
Implements a range of statistical methodology based on the negative binomial distributions,
including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood
tests. As well as RNA-seq, it can be applied to differential signal analysis of other types of genomic
data that produce counts, including ChIP-seq, Bisulfite-seq, SAGE and CAGE.
The tool can be applied to any technology that produces read counts for genomic features. Of
interest are summaries of short reads from massively parallel sequencing technologies such as
Illumina™, 454 or ABI SOLiD applied to RNA-Seq, SAGE-Seq or ChIP-Seq experiments, pooled shRNAseq or CRISPR-Cas9 genetic screens and bisulfite sequencing for DNA methylation studies. EdgeR
provides statistical routines for assessing differential expression in RNA-Seq experiments or
differential marking in ChIP-Seq experiments.
EdgeR can be applied to differential expression at the gene, exon, transcript or tag level. In fact,
read counts can be summarized by any genomic feature. EdgeR analyses at the exon level are easily
extended to detect differential splicing or isoform-specific differential expression.

This tool uses the edgeR quasi-likelihood pipeline (edgeR-quasi) for differential expression analysis.
This statistical methodology uses negative binomial generalized linear models, but with F-tests
instead of likelihood ratio tests. This method provides stricter error rate control than other negative
binomial based pipelines, including the traditional edgeR pipelines or DESeq2. While the limma
pipelines are recommended for large-scale datasets, because of their speed and flexibility, the
edgeR-quasi pipeline gives better performance in low-count situations.

  • New miRNA features:

miRNA feed forward loops

The miRNA feed forward loop is a combination of miRNA, a transcription factor and a target gene.
The miRNA regulates expression of the target gene. The transcription factor regulates transcription
of both: target gene and gene encoding the miRNA. This analysis accepts a list of miRNAs or a list of
target genes or both and finds corresponding miRNA feed forward loops. Results can be visualized
using ‘create miRNA diagram’ function.

Analyze miRNA target enrichment

This tool takes a set of human genes as input and searches for miRNA target enrichment with the
help of our in-house TargetScan database. The resource comprises miRNA/target gene links for
human based on conserved miRNA site prediction from TargetScan.

Get miRNA targets

This tool provides from a given list of human miRNAs their potential miRNA target genes with the
help of our in-house TargetScan database.
Create miRNA promoters

This tool creates a track (promoter sequence collection) from a list of given miRNAs.

  • More new features:

CR cluster selector

This method uses the result of a CRC (Chinese Restaurant Clustering) analysis and extracts most
centered cluster items into a separate table. More detailed, it sorts clusters by size, takes top
Maximum number of clusters to use with size greater than Min items per cluster and extracts Max
items per cluster items closest to the center of cluster.
Check Quotas

This method checks project disk space usage and corrects it with deleting temporary used disc space
if necessary.
Filter duplicate rows

This method filters duplicate rows from the input table and gives a non-redundant output.
Group table rows

This method helps to group selected rows from the input table. Output will contain a table with the
number of counts of the selected rows.
Merge Table columns

This method merges several columns of a table into one column using a selected aggregator.

Plot pie chart

This method creates a pie chart using a category column and a leading column for a visual evaluation
and comparison of the results. Colors for the different segments of the pie chart can be customized
using the color palate.
Plot bar chart

This method creates a bar chart using a category column and leading column for a visual evaluation
and comparison of the results. Colors for the different segments of the plot bar chart can be
customized using the color palate.

Select random rows

This method selects random rows from the input table to create a randomized output table based
on the selected random number of rows and percentage.
Select top rows

This method selects top rows based on the selected parameter from the input table. The rows can
be selected as top, middle or bottom types from the input table.
Super annotate table

This method allows to annotate columns in the input table from another user defined input table(s).
It can use more than one table as the source table to annotate different columns in the input table.

Transform table

This method changes/transforms the input table based on the selected operation. It can add the
selected operation (log2, log 10, Pow2, Pow10, exp) to the input table.
Tree map on functional classification

This analysis (REVIGO) was adapted and allows a tree map visualization of functional classification
results to reduce Gene Ontology terms and based on the p-value cut-off.

Compare diagrams

This method compares the structures of two diagrams based on the input parameters and gives
different entries within the resulting diagram.

Get molecules from diagrams

This analysis creates clones of selected nodes (protein names) for each its edge. It can be used to focus on
main interesting regulatory proteins and visualize results in the output clone diagram.

Find regulatory regions

This method creates promoter regions based on an input gene list (and based on Chip-seq peaks
located near the TSS if peaks are present). On top information from CAGE database (FANTOM5)
about most active TSSs in specific tissues or cell type can be used and promoter length to be
extracted can be defined. The result of this analysis can be used as input track for Site search
analysis.
Split VCF by regulation

This analysis separates an input VCF file into two sets: Yes-set – sites that do overlap with the
regulation track (= Out yes), No-set – sites, that do not. If the No-set contains less sites than defined
in the Min no size parameter (default = 100), random tracks from Default VCF will be added to the
No-set (=Out no).

MSAT

Motif Score Association Test (MSAT) is a tool to test for association between a motif score and a
quantity of interest using generalized linear models (glms).
For each TFBS motif of a specified profile, scores are calculated for promoter sequences of input
genes. R’s glm methodology is then applied to model the quantity of interest given with the input
genes as dependent variable or response (y) and motif scores as independent variable or predictors
(x):y=f(x).
For each motif the tool reports the estimated coefficient (slope) as well as its unadjusted and
adjusted p-values, where it is assumed that the results are most suitably ranked by (unadjusted or
adjusted) p-values.

Construct composite module on tracks with keynodes

Predicts composite module as Construct composite modules on tracks method AND uses Regulator
search analysis during calculating score of the composite module (score is used to select the best
module). Regulator search finds master-regulators which affect transcription factors included in the
modules.
Construct composite modules with keynodes

Predicts composite module as Construct composite modules method AND uses Regulator search
analysis during calculating score of the composite module (score is used to select the best module).
Regulator search finds master-regulators which affect transcription factors included in the modules.

 

RELEASE 4.9

  • New start page icons in any of the platform’s research categories
  • Pre-release of TRANSFAC®, TRANSPATH® and HumanPSD databases (version 2018.2)
  • Update to Ensembl 91 database
  • Update to Reactome 63 database

RELEASE 4.8

  • New analysis methods

Construct composite modules on track (correlation) – method predicts composite module using the result of the “Site search on gene set” analysis.

Cluster track – method clusters sites in a track, what is useful for merging of closely spaced sites into one big cluster.

Compute profile thresholds – method computes profile thresholds minimizing either false negatives(minFN) or false positive(minFP) on the random DNA sequence.

Create miRNA promoters – method extracts miRNA promoters from mirprom database for a given list of miRNAs

Get transcripts track – method extracts track from a database by a transcript ID

Recalculate composite module score on new track – method takes best composite model from the given CMA result and calculates its scores on all sites of a given track.

Continue CMA – method continues prediction of composite module using results of the previous prediction as a start point. Prediction parameters are customizable.

Table Imputation – method replaces missing data in the given input table with row means.

  • New HTML report for site search analysis

You can now create a summary of your site search analysis including visualization of input promoters together with identified enriched transcription factor binding sites (TFBSs) in HTML format, which can be exported to your local computer.

  • New toolbar buttons
  • Integration with updated TRANSFAC®, TRANSPATH® and HumanPSDTM databases in release 2018.1

RELEASE 4.7

Enhancement of the method LRPath.

Installation of TRANSFAC 2017.3 (information download)

– Annotation of transcription factor binding sites based on sequence conservation

ChIP-Seq experiment browse pages

– Reorganization of the in vivo transcription factor bound fragment section on a Locus Report

HOCOMOCO v10 matrix library integration

Enhanced human SNP content

Ensembl version update

Installation of TRANSPATH & HumanPSD 2017.3 (information download)

– Integration of new clinical trial (CT) data sources

– Improved user data management

– Quick search for disease and drug entries

– Link-out to BRENDA professional – the comprehensive enzyme information system

New phosphorylation targets content

RELEASE 4.6

LRPath is a Gene Set Enrichment Analysis (GSEA) method that uses logistic regression models to discover categories that are significantly correlated with a predictor.

New protein category (TRANSPATH® isogroups) to enhance identification of master regulators. This enhancement was updated to all workflows which included ‘Regulator search’ or ‘Effector search’ method.

RELEASE 4.5

Installation of TRANSFAC public:

– Available for everyone

– 219 profiles (matrices) for site search tools

– Search function implemented

DESeq tool:

– Bug fixed that prevented analysis from completing correctly

– Added option to run DESeq or DESeq2

HumanPSDTM:

– New versions of PROTEOMETM data now named HumanPSDTM database

– Latest release 2017.2 available in the geneXpain platform

– Platform Java API available from github.com/genexplain/genexplain-api

– Executable jar can be configured with JSON config files to invoke platform processes from the command line

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Demo Workflows

Here, we list workflows that were used to prove the capabilities of the geneXplain platform, for instance in the cited publications. The links given direct you straight into the platform without requiring any registration.
Using these demo workflows, you will be able to reproduce the published results and to learn more about the platform’s look and feel. To work with your own data, however, registration is required. Additional licensing is necessary for certain third-party products such as TRANSFAC® or TRANSPATH®.
Workflows 1-3 are from our recent publication Koschmann et al., Microarrays 4, 270-286.
1. Workflow “Identify enriched motifs in promoters“,
applied to datasets of naphthalene-treated mouse liver and lung tissue.
Find further instructions and explanations here.
Origin of datasets:
GEO GSE18858 and GSE17933
Thomas, R.S., et al. (2011) Application of transcriptional benchmark dose values in quantitative cancer and noncancer risk assessment. Toxicol. Sci. 120, 194-205. PMID: 21097997
Thomas, R.S., et al. (2009) Use of short-term transcriptional profiles to assess the long-term cancer-related safety of environmental and industrial chemicals.Toxicol. Sci. 112, 311-321. PMID: 19776212
2. Workflow “Find master regulators in the TRANSPATH® network“,
applied to datasets of naphthalene-treated mouse liver and lung tissue.
Find further instructions and explanations here.
The data sources are as for Workflow 1.
3. Workflow “Enriched upstream analysis with TRANSFAC® and TRANSPATH® network“,
applied to datasets of naphthalene-treated mouse liver and lung tissue.
Find further instructions and explanations here.
The data sources are as for Workflow 1.

Workflow management

Sequential launching of particular analysis modules can be saved as a graphically represented workflow. Modules are shown as purple rectangles, and outputs of each step serve as inputs into the next analysis step. A workflow that is specific for a given data set can be easily constructed by drag and drop of the required analysis modules. In addition, Java scripts and R scripts can be added directly within the platform, for more specific requirements of the analysis.
The picture shows a small workflow for the gene set enrichment analysis (GSEA) of using four different ontologies: Gene Ontology (GO) Biological Process, GO Cellular Compartment, GO Molecular Function, and Reactome's functional assignments (see on the right side). The larger light blue boxes are analysis functions (program modules, "Bricks"). Green boxes stand for input files, especially user-defined inputs. Yellow boxes represent automatic delivery or output files. A workflow can be intuitively designs by simple drag-and-drop of the constituents and graphically connecting them.

Workflow management in the geneXplain platform. (Click image to see the complete picture).

See demo workflows for a collection of executable workflows: no registration required!

Videos

Intro video of the geneXplain platform.

Information downloads

Publications

Blazquez R., Wlochowitz D., Wolff A., Seitz S., Wachter A., Perera-Bel J., Bleckmann A., Beißbarth T., Salinas G., Riemenschneider M.J., Proescholdt M., Evert M., Utpatel K., Siam L., Schatlo B., Balkenhol M., Stadelmann C., Schildhaus H.U., Korf U., Reinz E., Wiemann S., Vollmer E., Schulz M., Ritter U., Hanisch UK., Pukrop T. (2018) PI3K: A master regulator of brain metastasis-promoting macrophages/microglia. Glia. 66(11):2438-2455. doi: 10.1002/glia.23485. Epub 2018 Oct 25. Link

Orekhov, A. N., Oishi, Y., Nikiforov, N. G., Zhelankin, A. V., Dubrovsky, L, Sobenin, I. A., Kel, A., Stelmashenko, D., Makeev, V. J., Foxx, K., Jin, X., Kruth, H. S. and Bukrinsky, M. (2018) Modified Ldl Particles Activate Inflammatory Pathways In Monocyte-Derived Macrophages: Transcriptome Analysis. Curr. Pharm. Des., 11. doi: 10.2174/1381612824666180911120039. Link

 

Kalozoumi, G., Kel-Margoulis, O., Vafiadaki, E., Greenberg, D., Bernard, H., Soreq, H., Depaulis, A., Sanoudou, D. (2018) Glial responses during epileptogenesis in Mus musculus point to potential therapeutic targets. PLoS One. 13(8):e0201742. doi: 10.1371/journal.pone.0201742. Link

 

Smetanina, M.A., Kel, A.E., Sevost’ianova, K.S., Maiborodin, I.V., Shevela, A.I., Zolotukhin,  I.A., Stegmaier, P., Filipenko, M.L. (2018) DNA methylation and gene expression profiling reveal MFAP5 as a regulatory driver of extracellular matrix remodeling in varicose vein disease. Epigenomics. 10(8):1103-1119. doi: 10.2217/epi-2018-0001. Link

 

Boyarskikh, U., Pintus, S., Mandrik, N., Stelmashenko, D., Kiselev, I., Evshin, I., Sharipov, R., Stegmaier, P., Kolpakov, F., Filipenko, M., Kel, A. (2018) Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3. BMC Med Genomics. 11(Suppl 1):12. doi: 10.1186/s12920-018-0330-5. Link

 

Triska, M., Solovyev, V., Baranova, A., Kel, A., Tatarinova, T.V. (2017) Nucleotide patterns aiding in prediction of eukaryotic promoters. PLoS One. 12(11):e0187243. doi: 10.1371/journal.pone.0187243. Link

 

Niehof, M., Hildebrandt, T., Danov, O., Arndt, K., Koschmann, J., Dahlmann, F., Hansen, T. and Sewald, K. (2017) RNA isolation from precision-cut lung slices (PCLS) from different species. BMC Res. Notes 10, 121. doi: 10.1186/s13104-017-2447-6. Link

 

Mandić, A. D., Bennek, E., Verdier, J., Zhang, K., Roubrocks, S., Davis, R. J., Denecke, B., Gassler, N., Streetz, K., Kel, A., Hornef, M., Cubero, F. J., Trautwein, C. and Sellge, G. (2017) c-Jun N-terminal kinase 2 promotes enterocyte survival and goblet cell differentiation in the inflamed intestine. Mucosal Immunol. 10(5):1211-1223. doi: 10.1038/mi.2016.125. Link

 

Pietrzyńska, M., Zembrzuska, J., Tomczak, R., Mikołajczyk, J., Rusińska-Roszak, D., Voelkel, A., Buchwald, T., Jampílek, J., Lukáč, M., Devínsky, F. (2016) Experimental and in silico investigations of organic phosphates and phosphonates sorption on polymer-ceramic monolithic materials and hydroxyapatite. Eur. J. Pharm. Sci. 93, 295-303. doi: 10.1016/j.ejps.2016.08.033. Link

 

Kural, K. C., Tandon, N., Skoblov, M., Kel-Margoulis, O. V. and Baranova, A. V. (2016) Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence. BMC Genomics 17(Suppl 14), 1030. doi: 10.1186/s12864-016-3352-4. Link

 

Kel, A. E., Stegmaier, P., Valeev, T., Koschmann, J., Poroikov, V., Kel-Margoulis, O. V. and Wingender, E. (2016) Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. EuPA Open Proteomics 13, 1-13. doi: 10.1016/j.euprot.2016.09.002. Link

 

Ciribilli, Y., Singh, P., Inga, A., Borlak, J. (2016) c-Myc targeted regulators of cell metabolism in a transgenic mouse model of papillary lung adenocarcinoma. Oncotarget 7, 65514-65539. doi: 10.18632/oncotarget.11804. Link

 

Wlochowitz, D., Haubrock, M., Arackal, J., Bleckmann, A., Wolff, A., Beißbarth, T., Wingender, E., Gültas, M. (2016) Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines. Front. Genet. 7, 42. doi: 10.3389/fgene.2016.00042. Link

 

Lee, E.H., Oh, J.H., Selvaraj, S., Park, S.M., Choi, M.S., Spanel, R., Yoon, S. and Borlak, J. (2016) Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice. Oncotarget 7, 14983-15017. doi:10.18632/oncotarget.7698. Link

 

Borlak, J., Singh, P. and Gazzana, G. (2015) Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events. BMC Genomics 16, 124. doi:10.1186/s12864-015-1312-z. Link

 

Koschmann, J., Bhar, A., Stegmaier,P., Kel, A. E. and Wingender, E. (2015) “Upstream Analysis”: An integrated promoter-pathway analysis approach to causal interpretation of microarray data. Microarrays 4, 270-286. doi:10.3390/microarrays4020270. Link

 

Shi, Y., Nikulenkov, F., Zawacka-Pankau, J., Li, H., Gabdoulline, R., Xu, J., Eriksson, S., Hedström, E., Issaeva, N., Kel, A., Arnér, E.S., Selivanova, G. (2014) ROS-dependent activation of JNK converts p53 into an efficient inhibitor of oncogenes leading to robust apoptosis. Cell Death Differ. 21, 612-623. doi:10.1038/cdd.2013.186 Link

 

Schlereth, K., Heyl, C., Krampitz, A.M., Mernberger, M., Finkernagel, F., Scharfe, M., Jarek, M., Leich, E., Rosenwald, A., Stiewe, T. (2013) Characterization of the p53 Cistrome – DNA Binding Cooperativity Dissects p53’s Tumor Suppressor Functions. PLoS Genet. 9, e1003726. PubMed

 

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