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J-Express specifications

Information


Unique identifier OMICS_00767
Name J-Express
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input format TXT
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

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  • person_outline J-Express Team <>

Publications for J-Express

J-Express in pipelines

 (8)
2017
PMCID: 5294893
PMID: 28173797
DOI: 10.1186/s12885-017-3109-8

[…] the log-rank test. a p-value < 0.05 was considered significant. differentially expressed genes were identified between pairs of sample groups, utilising unpaired sam [] analysis implemented in j-express [], with 1000 permutations, and considering the list of genes with q < 0.05 as significantly differentially expressed., gene ontology overrepresentation analysis was performed […]

2017
PMCID: 5586053
PMID: 28877686
DOI: 10.1186/s12885-017-3620-y

[…] the humanht-12 v4 beadchip targets 47,231 probes that are mainly derived from genes in the ncbi refseq database (release 38)., data from the array scanning were investigated in genomestudio and j-express 2012 for quality control measures []. all arrays within each experiment were quantile normalized to be comparable before being compiled into an expression profile data matrix. the probe […]

2015
PMCID: 4333900
PMID: 25765704
DOI: 10.1186/s12864-015-1277-y

[…] resolution of five μm with settings outlined in the protocol. data were extracted using agilent feature extraction software 9.5.3 as described in instructions. analysis of data has been performed in j-express (version 2009) software package []. to identify genes that are significantly differentially expressed between groups significance analysis of microarrays (sam) [] has been used on log2 […]

2015
PMCID: 4535937
PMID: 26484203
DOI: 10.1016/j.gdata.2015.04.010

[…] hospital, norway). for each sample 6 biological replicates were analyzed. data extraction and quality control was performed in genomestudio (illumina) and the data analysis was performed using j-express ., to identify the most differentially expressed genes between wild type bxpc-3 cells and the β-catenin gene disrupted clones #4 and #111 (average) significance analysis of microarrays […]

2014
PMCID: 4275244
PMID: 25536063
DOI: 10.1371/journal.pone.0115496

[…] hospital, norway). for each sample 6 biological replicates were analyzed. data extraction and quality control was performed in genomestudio (illumina) and the data analysis was performed using j-express . ontology enrichment analysis was done using david with the goterm_bp_2 annotation. the results from the microarray analysis have been deposited to the gene expression omnibus repository […]


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J-Express in publications

 (126)
PMCID: 5941969
PMID: 29770133
DOI: 10.3389/fimmu.2018.00845

[…] mann–whitney u test and the chi square test for comparison of unpaired groups. correlations between continuous variables are given as the kendall’s tau-b coefficient with corresponding p-value. j-express (molmine as, bergen, norway) was applied for bioinformatics analyses (). time to reconstitution was analyzed with the kaplan–meier survival method with the log-rank test, cox regression […]

PMCID: 5897503
PMID: 29681903
DOI: 10.3389/fimmu.2018.00691

[…] and complete linkage gives the best homology between mediator concentrations and the most compact clusters when running the clustering analysis (–)., clustering analyzes were carried out using j-express (molmine as, bergen, norway) (). other statistical analyzes were performed using graph pad prism 5 (graph pad software, inc., san diego, ca, usa) and spss (version 20, release 20.0.0.2, ibm […]

PMCID: 5869700
PMID: 29588496
DOI: 10.1038/s41598-018-23667-x

[…] 5 kb. following assembly transcripts were annotated with blast matches, protein domains and go terms using the trinotate toolkit (https://trinotate.github.io)., gene ontology mapping was performed in j-express gene expression analysis software. detailed information about the gene included in each category was obtained using quick go, which is a fast browser for gene ontology terms and annotation ( […]

PMCID: 5793460
PMID: 29386057
DOI: 10.1186/s13287-018-0778-4

[…] cycle (ct) was used to calculate the 2–δct value for each gene using pcr array data analysis web portal (sabiosciences). 2–δct values were then exported to microarray data analysis software (j-express 2012). for statistical analysis, unsupervised hierarchical clustering and one-way analysis of variance (anova) with bonferroni post hoc analysis were used., three hundred nanograms of total […]

PMCID: 5789820
PMID: 29382956
DOI: 10.1038/s41598-018-20308-1

[…] and mapped with bowtie2 and normalized by total read counts. expression of kegg hippo pathway genes in testis and selected hippo genes in other tissues were illustrated with heatmaps made with j-express v. 2012, using high level mean and variance normalization, and clustered with complete linkage and euclidean distance measure., all rna isolation prior to qpcr was done using iprep total […]


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J-Express institution(s)
University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway; Computational Biology Unit, BCCS, University of Bergen, Bergen, Norway; MolMine AS, Thormoehlens, Bergen, Norway

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