Integrated Transcriptome Map Highlights Structural and Functional Aspects of the Normal Human Heart

Caracausi, Maria; Piovesan, Allison; Vitale, Lorenza; Pelleri, Maria Chiara

doi:10.1002/jcp.25471

Cited by 14 publications

(25 citation statements)

References 60 publications

(76 reference statements)

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“…From this particular point of view, the presented results are less systematic than other previous attempts conducted in the case of the brain (34) and heart (14). Only the samples belonging to experiments in which a series of normal human tissues were analyzed have been included here, without searching for any single samples recorded for a given tissue in any type of available experiment (for example, comparisons between normal and pathological samples).…”

Section: Discussioncontrasting

confidence: 69%

“…The query used was: ‘Homo sapiens [ORGANISM] AND tissue* [TI] OR organ* [TI]’. These selection criteria led to the generation of a pool of samples that included all of the main human organs and tissues, which served as a reference set already partially used by the authors of the present study (14). The searches were performed up to May 2013, and search results were then filtered using inclusion and exclusion criteria as explained in the Data set selection subsection below.…”

Section: Methodsmentioning

confidence: 99%

“…This set included 629 samples described previously (14), which were in addition to the following GEO samples: GSM2829, GSM2856, GSM18792, GSM18793, GSM18951, GSM18952, GSM39975, GSM39980, GSM39992, GSM39994, GSM39999, GSM40001, GSM44671, GSM52565, GSM175935, GSM790822 and GSM790831. These samples were pre-processed according to the TRAM tool guide to be ready for import and processing in TRAM.…”

Section: Methodsmentioning

confidence: 99%

“…TRAM can integrate data from hundreds or thousands of complete microarray data sets and provide unique combinations of features that are particularly suited to allow the choice of reference genes based on the three properties aforementioned. TRAM calculates a quantitative measurement for a consensus mean-expression value for tens of thousands of human transcripts expressed in a specific tissue or organ, thus allowing for a precise estimation of the intensity of its expression in terms of a percentage of the mean expression value in the pool of analyzed transcriptomes and the choice of a reference gene expressed at medium-high or high level (12,14). In addition, TRAM provides the standard deviation (SD) from the mean (normalized as the percentage of the mean value) for the mean expression value of a given locus, thus allowing for the selection of genes that may have more stable expression values in a variety of different samples and/or experimental platforms that have been investigated for a given tissue/organ.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies

Caracausi

Piovesan

Antonaros

et al. 2017

Molecular Medicine Reports

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The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium-high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes. Recent advancements in the quality and completeness of human expression microarray data and in their statistical analysis may provide new clues toward the quantitative standardization of human gene expression studies in biology and medicine, both cross- and within-tissue. The systematic approach used by the present study is based on the Transcriptome Mapper tool and exploits the automated reassignment of probes to corresponding genes, intra- and inter-sample normalization, elaboration and representation of gene expression values in linear form within an indexed and searchable database with a graphical interface recording quantitative levels of expression, expression variability and cross-tissue width of expression for more than 31,000 transcripts. The present study conducted a meta-analysis of a pool of 646 expression profile data sets from 54 different human tissues and identified actin γ 1 as the HK gene that best fits the combination of all the traditional criteria to be used as a reference gene for general use; two ribosomal protein genes, RPS18 and RPS27, and one aquaporin gene, POM121 transmembrane nucleporin C, were also identified. The present study provided a list of tissue- and organ-specific genes that may be most suited for the following individual tissues/organs: Adipose tissue, bone marrow, brain, heart, kidney, liver, lung, ovary, skeletal muscle and testis; and also provides in these cases a representative, quantitative portrait of the relative, typical gene-expression profile in the form of searchable database tables.

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Section: Discussioncontrasting

confidence: 69%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies

Caracausi

Piovesan

Antonaros

et al. 2017

Molecular Medicine Reports

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show abstract

“…The absolute size, however, may vary across a range of variation of four orders of magnitude (10 000 times). Using an original method for transcriptome mapping (24), including systematic UniGene based conversion of gene identifiers (25), the estimation of the average human gene length was useful in order to determine the significance of over- or under-expressed genomic segments equivalent to single gene size in the whole normal human heart transcriptome map (26). …”

Section: Discussionmentioning

confidence: 99%

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

et al. 2016

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We release GeneBase 1.1, a local tool with a graphical interface useful for parsing, structuring and indexing data from the National Center for Biotechnology Information (NCBI) Gene data bank. Compared to its predecessor GeneBase (1.0), GeneBase 1.1 now allows dynamic calculation and summarization in terms of median, mean, standard deviation and total for many quantitative parameters associated with genes, gene transcripts and gene features (exons, introns, coding sequences, untranslated regions). GeneBase 1.1 thus offers the opportunity to perform analyses of the main gene structure parameters also following the search for any set of genes with the desired characteristics, allowing unique functionalities not provided by the NCBI Gene itself. In order to show the potential of our tool for local parsing, structuring and dynamic summarizing of publicly available databases for data retrieval, analysis and testing of biological hypotheses, we provide as a sample application a revised set of statistics for human nuclear genes, gene transcripts and gene features. In contrast with previous estimations strongly underestimating the length of human genes, a ‘mean’ human protein-coding gene is 67 kbp long, has eleven 309 bp long exons and ten 6355 bp long introns. Median, mean and extreme values are provided for many other features offering an updated reference source for human genome studies, data useful to set parameters for bioinformatic tools and interesting clues to the biomedical meaning of the gene features themselves.Database URL: http://apollo11.isto.unibo.it/software/

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Human trisomy 21 fibroblasts rescue methotrexate toxic effect after treatment with 5‐methyl‐tetrahydrofolate and 5‐formyl‐tetrahydrofolate

Vitale

Serpieri

Lauriola

et al. 2019

Journal Cellular Physiology

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Trisomy 21 causes Down syndrome (DS), the most common human genetic disorder and the leading genetic cause of intellectual disability. The alteration of one‐carbon metabolism was described as the possible metabolic cause of the intellectual disability development in subjects with DS. One of the biochemical pathways involved in the one‐carbon group transfer is the folate cycle. The cytotoxic drug methotrexate (MTX) is a folic acid (FA) analogue which inhibits the activity of dihydrofolate reductase enzyme involved in the one‐carbon metabolic cycle. Trisomy 21 cells are more sensitive to the MTX effect than euploid cells, and in 1986 Jérôme Lejeune and Coll. demonstrated that MTX was twice as toxic in trisomy 21 lymphocytes than in control cells. In the present work, the rescue effect on MTX toxicity mediated by FA and some of its derivatives, tetrahydrofolate (THF), 5‐formyl‐THF, and 5‐methyl‐THF, in both normal and trisomy 21 skin fibroblast cells, was evaluated. A statistically significant rescue effect was obtained by 5‐formyl‐THF, 5‐methyl‐THF, and their combination, administered together with MTX. In conclusion, trisomy 21 fibroblast cell lines showed a good response to the rescue effects of 5‐formyl‐THF and 5‐methyl‐THF on the MTX toxicity almost as normal cell lines.

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Integrated Transcriptome Map Highlights Structural and Functional Aspects of the Normal Human Heart

Cited by 14 publications

References 60 publications

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

Human trisomy 21 fibroblasts rescue methotrexate toxic effect after treatment with 5‐methyl‐tetrahydrofolate and 5‐formyl‐tetrahydrofolate

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