CoPub: a literature-based keyword enrichment tool for microarray data analysis

Frijters, Raoul; Heupers, Bart; Beek, Pieter van; Bouwhuis, M.; Schaik, René C. van; Vlieg, Jacob de; Polman, Jan; Alkema, Wynand

doi:10.1093/nar/gkn215

Cited by 73 publications

(48 citation statements)

References 22 publications

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“…pathways, diseases, drugs, and Gene Ontology (GO) terms) from literature (34,35) was used to substantiate the transcriptomics findings. CoPub calculates an R-scaled score between two co-occurring concepts (i.e.…”

Section: Methodsmentioning

confidence: 99%

Interorgan Coordination of the Murine Adaptive Response to Fasting

Hakvoort

Moerland

Frijters

et al. 2011

Journal of Biological Chemistry

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Starvation elicits a complex adaptive response in an organism.No information on transcriptional regulation of metabolic adaptations is available. We, therefore, studied the gene expression profiles of brain, small intestine, kidney, liver, and skeletal muscle in mice that were subjected to 0 -72 h of fasting. Functional-category enrichment, text mining, and network analyses were employed to scrutinize the overall adaptation, aiming to identify responsive pathways, processes, and networks, and their regulation. The observed transcriptomics response did not follow the accepted "carbohydrate-lipid-protein" succession of expenditure of energy substrates. Instead, these processes were activated simultaneously in different organs during the entire period. The most prominent changes occurred in lipid and steroid metabolism, especially in the liver and kidney. They were accompanied by suppression of the immune response and cell turnover, particularly in the small intestine, and by increased proteolysis in the muscle. The brain was extremely well protected from the sequels of starvation. 60% of the identified overconnected transcription factors were organ-specific, 6% were common for 4 organs, with nuclear receptors as protagonists, accounting for almost 40% of all transcriptional regulators during fasting. The common transcription factors were PPAR␣, HNF4␣, GCR␣, AR (androgen receptor), SREBP1 and -2, FOXOs, EGR1, c-JUN, c-MYC, SP1, YY1, and ETS1. Our data strongly suggest that the control of metabolism in four metabolically active organs is exerted by transcription factors that are activated by nutrient signals and serves, at least partly, to prevent irreversible brain damage.Adapting to starvation requires an interorgan integration of the activity of metabolic pathways to protect the body from an irreversible loss of resources (1, 2), but how the organism integrates these reactions remains largely unknown. Numerous studies on humans, who fasted for 3-6 weeks, have shown that glycogen stores are depleted within a day (3). The decline in circulating glucose and insulin during the next few days (4) induces a transient increase in plasma (essential) amino acids and a concomitant decline in plasma alanine levels due to an increased hepatic extraction for gluconeogenesis (5, 6). Muscle catabolism is a major source of amino acids in this phase. When fasting is continued, muscle protein catabolism declines, and hepatic uptake of amino acids decreases, which is reflected in a decline of endogenous glucose production (6) and urinary nitrogen excretion (4, 7). Lipid catabolism and the (hepatic) production of ketone bodies also increases rapidly and is quantitatively similar after 3 days and 5-6 weeks of starvation (8), but plasma levels increase only gradually to plateau after 4 weeks (4, 9). The associated increase in urinary ketone body (organic-acid) excretion requires a compensatory increase in ammonia production and urinary excretion (4, 7, 10), which is met by an increased renal amino acid uptake and gluconeogenesis (5, 6)...

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Section: Methodsmentioning

confidence: 99%

Interorgan Coordination of the Murine Adaptive Response to Fasting

Hakvoort

Moerland

Frijters

et al. 2011

Journal of Biological Chemistry

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“…Classification of DEGs and identification of quantitatively enriched functional categories were done using different tools of the Database for Annotation, Visualization, and Integrated Discovery (DAVID) [45]. Identification of biological keywords cocited with DEGs in PubMed abstracts was performed with CoPub [46]. Analysis of functional databases was based on the Entrez Gene ID of the putative human orthologous genes.…”

Section: Affymetrix Genechip Hybridization and Data Analysismentioning

confidence: 99%

Comparison of the Effects of Early Pregnancy with Human Interferon, Alpha 2 (IFNA2), on Gene Expression in Bovine Endometrium1

Bauersachs¹,

Ulbrich

Reichenbach

et al. 2012

Biology of Reproduction

109

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Interferon tau (IFNT), a type I IFN similar to alpha IFNs (IFNA), is the pregnancy recognition signal produced by the ruminant conceptus. To elucidate specific effects of bovine IFNT and of other conceptus-derived factors, endometrial gene expression changes during early pregnancy were compared to gene expression changes after intrauterine application of human IFNA2. In experiment 1, endometrial tissue samples were obtained on Day (D) 12, D15, and D18 postmating from nonpregnant or pregnant heifers. In experiment 2, heifers were treated from D14 to D16 of the estrous cycle with an intrauterine device releasing IFNA2 or, as controls, placebo lipid extrudates or PBS only. Endometrial biopsies were performed after flushing the uterus. All samples from both experiments were analyzed with an Affymetrix Bovine Genome Array. Experiment 1 revealed differential gene expression between pregnant and nonpregnant endometria on D15 and D18. In experiment 2, IFNA2 treatment resulted in differential gene expression in the bovine endometrium. Comparison of the data sets from both studies identified genes that were differentially expressed in response to IFNA2 but not in response to pregnancy on D15 or D18. In addition, genes were found that were differentially expressed during pregnancy but not after IFNA2 treatment. In experiment 3, spatiotemporal alterations in expression of selected genes were determined in uteri from nonpregnant and early pregnant heifers using in situ hybridization. The overall findings of this study suggest differential effects of bovine IFNT compared to human IFNA2 and that some pregnancy-specific changes in the endometrium are elicited by conceptus-derived factors other than IFNT.endometrium, hormone action, pregnancy, reproductive immunology, uterus

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“…The text-mining tool CoPub (Frijters et al 2008) was used to identify biological keywords associated with the differentially expressed genes. These analyses were all based on the Entrez Gene ID of the putative human orthologous genes.…”

Section: Microarray Hybridisation and Data Analysismentioning

confidence: 99%

Gene expression profiling of bovine peripartal placentomes: detection of molecular pathways potentially involved in the release of foetal membranes

Streyl¹,

Kenngott²,

Herbach³

et al. 2012

Reproduction

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The mechanisms underlying detachment of foetal membranes after birth in cows are still unclear. To address this problem in a systematic manner, we performed the first holistic transcriptome study of bovine placentomes antepartum (AP; nZ4 cows) and intrapartum (IP; nZ4 cows) using Affymetrix GeneChip Bovine Genome Arrays. Three placentomes were extracted from each cow, and tissue samples from the contact zones of the placentomes (foeto-maternal units) were recovered by systematic random sampling and processed for RNA extraction and for stereological quantification of cellular composition. Statistical analysis of microarray data (false discovery rate 1%) revealed 759 mRNAs with at least twofold higher levels in the samples of the AP group, whereas 514 mRNAs showed higher levels in the IP group. The differentially expressed genes were classified according to biological processes and molecular functions using the Functional Annotation Clustering tool of the DAVID Bioinformatics Resources. Genes with higher mRNA levels in the AP group were nearly completely related to mitotic cell cycle and tissue differentiation. During parturition, a complete shift occurred because the genes with higher mRNA levels in IP were nearly all related to three different physiological processes/complexes: i) apoptosis, ii) degradation of extra cellular matrix and iii) innate immune response, which play a fundamental role in placental detachment. These results are an excellent basis for future studies investigating the molecular basis of retained foetal membranes.

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CoPub: a literature-based keyword enrichment tool for microarray data analysis

Cited by 73 publications

References 22 publications

Interorgan Coordination of the Murine Adaptive Response to Fasting

Interorgan Coordination of the Murine Adaptive Response to Fasting

Comparison of the Effects of Early Pregnancy with Human Interferon, Alpha 2 (IFNA2), on Gene Expression in Bovine Endometrium1

Gene expression profiling of bovine peripartal placentomes: detection of molecular pathways potentially involved in the release of foetal membranes

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