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  • 1
    Language: English
    In: PLoS ONE, 01 January 2017, Vol.12(11), p.e0188274
    Description: Analysis of data measured on different scales is a relevant challenge. Biomedical studies often focus on high-throughput datasets of, e.g., quantitative measurements. However, the need for integration of other features possibly measured on different scales, e.g. clinical or cytogenetic factors, becomes increasingly important. The analysis results (e.g. a selection of relevant genes) are then visualized, while adding further information, like clinical factors, on top. However, a more integrative approach is desirable, where all available data are analyzed jointly, and where also in the visualization different data sources are combined in a more natural way. Here we specifically target integrative visualization and present a heatmap-style graphic display. To this end, we develop and explore methods for clustering mixed-type data, with special focus on clustering variables. Clustering of variables does not receive as much attention in the literature as does clustering of samples. We extend the variables clustering methodology by two new approaches, one based on the combination of different association measures and the other on distance correlation. With simulation studies we evaluate and compare different clustering strategies. Applying specific methods for mixed-type data proves to be comparable and in many cases beneficial as compared to standard approaches applied to corresponding quantitative or binarized data. Our two novel approaches for mixed-type variables show similar or better performance than the existing methods ClustOfVar and bias-corrected mutual information. Further, in contrast to ClustOfVar, our methods provide dissimilarity matrices, which is an advantage, especially for the purpose of visualization. Real data examples aim to give an impression of various kinds of potential applications for the integrative heatmap and other graphical displays based on dissimilarity matrices. We demonstrate that the presented integrative heatmap provides more information than common data displays about the relationship among variables and samples. The described clustering and visualization methods are implemented in our R package CluMix available from https://cran.r-project.org/web/packages/CluMix.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 2
    Language: English
    In: PLoS ONE, 2010, Vol.5(2), p.e9022
    Description: Potential regulators of adipogenesis include microRNAs (miRNAs), small non-coding RNAs that have been recently shown related to adiposity and differentially expressed in fat depots. However, to date no study is available, to our knowledge, regarding miRNAs expression profile during human adipogenesis. Thereby, the aim of this study was to investigate whether miRNA pattern in human fat cells and subcutaneous adipose tissue is associated to obesity and co-morbidities and whether miRNA expression profile in adipocytes is linked to adipogenesis. ; We performed a global miRNA expression microarray of 723 human and 76 viral mature miRNAs in human adipocytes during differentiation and in subcutaneous fat samples from non-obese (n = 6) and obese with (n = 9) and without (n = 13) Type-2 Diabetes Mellitus (DM-2) women. Changes in adipogenesis-related miRNAs were then validated by RT-PCR. Fifty of 799 miRNAs (6.2%) significantly differed between fat cells from lean and obese subjects. Seventy miRNAs (8.8%) were highly and significantly up or down-regulated in mature adipocytes as compared to pre-adipocytes. Otherwise, 17 of these 799 miRNAs (2.1%) were correlated with anthropometrical (BMI) and/or metabolic (fasting glucose and/or triglycerides) parameters. We identified 11 miRNAs (1.4%) significantly deregulated in subcutaneous fat from obese subjects with and without DM-2. Interestingly, most of these changes were associated with miRNAs also significantly deregulated during adipocyte differentiation. ; The remarkable inverse miRNA profile revealed for human pre-adipocytes and mature adipocytes hints at a closely crosstalk between miRNAs and adipogenesis. Such candidates may represent biomarkers and therapeutic targets for obesity and obesity-related complications.
    Keywords: Research Article ; Cell Biology ; Diabetes And Endocrinology ; Cell Biology -- Cell Signaling ; Cell Biology -- Gene Expression ; Developmental Biology -- Cell Differentiation ; Genetics And Genomics -- Genetics Of Disease ; Diabetes And Endocrinology -- Obesity
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: The Journal of Urology, 2010, Vol.184(5), pp.1888-1894
    Description: Surgical resection remains the most effective treatment in patients with pulmonary metastasis of renal cell carcinoma. To our knowledge the prognostic significance of mediastinal and hilar lymph node metastasis during pulmonary metastasectomy in patients with renal cell carcinoma is unknown. We analyzed the value of computerized tomography to predict mediastinal/hilar lymph node involvement as well as the impact of systematic lymphadenectomy on survival in patients with pulmonary renal cell carcinoma metastasis. We analyzed survival in 110 patients who underwent resection of pulmonary metastasis of renal cell carcinoma using the Kaplan-Meier method. Multivariate analysis was done by Cox regression analysis. Lymph node metastasis was histologically proved in 35% of patients. Metastasis was not associated with initial tumor grade, lymph node status, the number of pulmonary metastases or recurrent pulmonary metastasis. Computerized tomography had 84% sensitivity and 97% specificity to predict lymph node metastasis. Sensitivity was markedly better for detecting mediastinal than hilar lymph node metastasis (90% vs 69%). Patients with lymph node metastasis had significantly shorter median survival than patients without lymph node metastasis (19 vs 102 months, p 〈0.001). Multivariate analysis revealed that tumor infiltrated mediastinal lymph nodes were an independent prognostic factor for patient survival. Match paired analysis showed that after lymph node dissection patients showed a trend toward improved survival. Mediastinal and hilar lymph node metastases significantly correlate with decreased survival. Systematic lymphadenectomy provides valuable information on staging and prognosis in patients with pulmonary metastasis of renal cell carcinoma, and may prolong survival.
    Keywords: Kidney ; Carcinoma ; Renal Cell ; Lymph Node Dissection ; Lung ; Neoplasm Metastasis ; Medicine
    ISSN: 0022-5347
    E-ISSN: 1527-3792
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  • 4
    In: Biometrical Journal, March 2018, Vol.60(2), pp.381-394
    Description: Interrater agreement on binary measurements with more than two raters is often assessed using Fleiss' κ, which is known to be difficult to interpret. In situations where the same raters rate all items, however, the far less known κ suggested by Conger, Hubert, and Schouten is more appropriate. We try to support the interpretation of these characteristics by investigating various models or scenarios of rating. Our analysis, which is restricted to binary data, shows that conclusions concerning interrater agreement by κ heavily depend on the population of items or subjects considered, even if the raters have identical behavior. The standard scale proposed by Landis and Koch, which verbally interprets numerical values of κ, appears to be rather subjective. On the basis of one of the models for rater behavior, we suggest an alternative verbal interpretation for kappa. Finally, we reconsider a classical example from pathology to illustrate the application of our methods and models. We also look for subgroups of raters with similar rating behavior using hierarchical clustering.
    Keywords: Binary Ratings ; Carcinoma Data ; Conger–Hubert–Schouten Kappa ; Fleiss’ Kappa ; Modeling Rater Behavior
    ISSN: 0323-3847
    E-ISSN: 1521-4036
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  • 5
    In: Bioinformatics, 2011, Vol. 27(9), pp.1316-1317
    Description: Summary: TEQC is an R/Bioconductor package for quality assessment of target enrichment experiments. Quality measures comprise specificity and sensitivity of the capture, enrichment, per-target read coverage and its relation to hybridization probe characteristics, coverage uniformity and reproducibility, and read duplicate analysis. Several diagnostic plots allow visual inspection of the data quality. is implemented in the R language (version 〉2.12.0) and is available as a Bioconductor package for Linux, Windows and MacOS from . 〈p〉〈bold〉Contact:〈/bold〉 〈email〉manuela.hummel@crg.es〈/email〉〈/p〉
    Keywords: Biology;
    ISSN: 1367-4803
    E-ISSN: 1460-2059
    E-ISSN: 13674811
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  • 6
    Language: English
    In: https://doi.org/10.1186/s12864-016-2623-4
    Description: Abstract Background: cAMP signaling produces dramatic changes in astrocyte morphology and physiology. However, its involvement in phenotype acquisition and the transcriptionally mediated mechanisms of action are largely unknown. Results: Here we analyzed the global transcriptome of cultured astroglial cells incubated with activators of cAMP pathways. A bulk of astroglial transcripts, 6221 annotated genes, were differentially regulated by cAMP signaling. cAMP analogs strongly upregulated genes involved in typical functions of mature astrocytes, such as homeostatic control, metabolic and structural support to neurons, antioxidant defense and communication, whereas they downregulated a considerable number of proliferating and immaturity-related transcripts. Moreover, numerous genes typically activated in reactive cells, such as scar components and immunological mediators, were repressed by cAMP. GSEA analysis contrasting gene expression profiles with transcriptome signatures of acutely isolated astrocytes and in situ evaluation of protein levels in these cells showed that cAMP signaling conferred mature and in vivo-like transcriptional features to cultured astrocytes. Conclusions: These results indicate that cAMP signaling is a key pathway promoting astrocyte maturation and restricting their developmental and activation features. Therefore, a positive modulation of cAMP signaling may promote the normal state of differentiated astrocytes and favor the protection and function of neuronal networks. Keywords: Antioxidant defense, Astrocytes, cAMP, Differentiation, Reactive glia, Transcriptomic, Brain, NR2C
    Keywords: Antidiabètics ; Astròcits ; Hypoglucemic Agents ; Astrocytes
    ISSN: 1471-2164
    Source: Universitat de Barcelona
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  • 7
    Language: English
    Description: BACKGROUND: cAMP signaling produces dramatic changes in astrocyte morphology and physiology. However, its involvement in phenotype acquisition and the transcriptionally mediated mechanisms of action are largely unknown. RESULTS: Here we analyzed the global transcriptome of cultured astroglial cells incubated with activators of cAMP pathways. A bulk of astroglial transcripts, 6221 annotated genes, were differentially regulated by cAMP signaling. cAMP analogs strongly upregulated genes involved in typical functions of mature astrocytes, such as homeostatic control, metabolic and structural support to neurons, antioxidant defense and communication, whereas they downregulated a considerable number of proliferating and immaturity-related transcripts. Moreover, numerous genes typically activated in reactive cells, such as scar components and immunological mediators, were repressed by cAMP. GSEA analysis contrasting gene expression profiles with transcriptome signatures of acutely isolated astrocytes and in situ evaluation of protein levels in these cells showed that cAMP signaling conferred mature and in vivo-like transcriptional features to cultured astrocytes. CONCLUSIONS: These results indicate that cAMP signaling is a key pathway promoting astrocyte maturation and restricting their developmental and activation features. Therefore, a positive modulation of cAMP signaling may promote the normal state of differentiated astrocytes and favor the protection and function of neuronal networks.
    Keywords: Antioxidants ; Antioxidant defense ; Astrocytes ; Brain ; Differentiation ; NR2C ; Reactive glia ; Transcriptomic ; cAMP
    ISSN: 1471-2164
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  • 8
    Language: English
    In: The Journal of experimental biology, 01 November 2011, Vol.214(Pt 21), pp.3596-604
    Description: In the auditory system of bushcrickets, sound can reach the receptors via two different paths: (i) by acting on the outside of the tympana situated on both sides of each foreleg or (ii) through the acoustic trachea that opens at a spiracle on the thorax. While the spiracle is considered to be the main point of sound entry for higher audio and ultrasonic frequencies, the role of the tympana is still unclear. The tympana border the air-filled acoustic trachea as well as the fluid-filled haemolymph channel containing the receptor organs. To understand their role during sound transduction, the sound-induced neuronal response of the hearing organ was recorded in combination with measurement of tympanal membrane motion using laser-Doppler vibrometry. For far-field stimulation, the frequency of the most sensitive hearing (∼16 kHz) matched the frequency of a pronounced maximum of tympanal membrane vibration. A second maximum of tympanum motion at lower frequencies (∼7 kHz) was correlated with an increased nerve activity at higher intensities (〉70 dB sound pressure level, SPL). These correlations support the hypothesis of functional coupling between tympanum motion and nerve activity. When sound stimuli were applied locally, through either the tympanum or the spiracle, significant differences between tympanum motion and nerve activity were found. These discrepancies show that tympanum motion and neuronal response are not coupled directly and that there is no linear relationship with the applied SPL. Taken together, these data verify a functional, albeit indirect, coupling of tympanum motion and sensory cell activity for one of the pronounced vibration maxima, which appears to represent a resonance frequency of the tympanum.
    Keywords: Extremities ; Cochlear Nerve -- Physiology ; Gryllidae -- Physiology ; Hearing -- Physiology ; Tympanic Membrane -- Physiology
    ISSN: 00220949
    E-ISSN: 1477-9145
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  • 9
    Language: English
    In: BMC Genomics, June 23, 2011, Vol.12, p.326
    Description: Background Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer. Results By applying a procedure for cross-platform data meta-analysis based on RankProd and GlobalAncova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We use this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we find an entirely new set of genes previously unrelated to the currently accepted EGF associated cellular functions. Conclusions We propose that the use of global genomic cross-validation derived from high content technologies (microarrays or deep sequencing) can be used to generate more reliable datasets. This approach should help to improve the confidence of downstream in silico functional inference analyses based on high content data.
    Keywords: Epidermal Growth Factors -- Properties ; Dna Sequencing -- Methods ; Genomes -- Identification And Classification ; Dna Microarrays -- Usage
    ISSN: 1471-2164
    Source: Cengage Learning, Inc.
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  • 10
    Language: English
    In: BMC Genomics, June 23, 2011, Vol.12, p.326
    Description: Background Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer. Results By applying a procedure for cross-platform data meta-analysis based on RankProd and GlobalAncova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We use this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we find an entirely new set of genes previously unrelated to the currently accepted EGF associated cellular functions. Conclusions We propose that the use of global genomic cross-validation derived from high content technologies (microarrays or deep sequencing) can be used to generate more reliable datasets. This approach should help to improve the confidence of downstream in silico functional inference analyses based on high content data.
    Keywords: Epidermal Growth Factors -- Properties ; Dna Sequencing -- Methods ; Genomes -- Identification And Classification ; Dna Microarrays -- Usage
    ISSN: 1471-2164
    Source: Cengage Learning, Inc.
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