scholarly journals Parallel protein and transcript profiles of FSHD patient muscles correlate to the D4Z4 arrangement and reveal a common impairment of slow to fast fibre differentiation and a general deregulation of MyoD-dependent genes

PROTEOMICS ◽  
2006 ◽  
Vol 6 (19) ◽  
pp. 5303-5321 ◽  
Author(s):  
Barbara Celegato ◽  
Daniele Capitanio ◽  
Mario Pescatori ◽  
Chiara Romualdi ◽  
Beniamina Pacchioni ◽  
...  
Keyword(s):  
Fshd Patient ◽  
Fast Fibre ◽  
Transcript Profiles

scholarly journals sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling

2021 ◽  
Author(s):  
Alma Andersson ◽  
Joakim Lundeberg
Keyword(s):  
Spatial Patterns ◽  
Expression Profiles ◽  
Synthetic Data ◽  
Real Data ◽  
Cell Types ◽  
Statistical Hypothesis ◽  
Supplementary Information ◽  
Statistical Hypothesis Testing ◽  
Transcriptomics Data ◽  
Transcript Profiles

Abstract Motivation Collection of spatial signals in large numbers has become a routine task in multiple omics-fields, but parsing of these rich datasets still pose certain challenges. In whole or near-full transcriptome spatial techniques, spurious expression profiles are intermixed with those exhibiting an organized structure. To distinguish profiles with spatial patterns from the background noise, a metric that enables quantification of spatial structure is desirable. Current methods designed for similar purposes tend to be built around a framework of statistical hypothesis testing, hence we were compelled to explore a fundamentally different strategy. Results We propose an unexplored approach to analyze spatial transcriptomics data, simulating diffusion of individual transcripts to extract genes with spatial patterns. The method performed as expected when presented with synthetic data. When applied to real data, it identified genes with distinct spatial profiles, involved in key biological processes or characteristic for certain cell types. Compared to existing methods, ours seemed to be less informed by the genes’ expression levels and showed better time performance when run with multiple cores. Availabilityand implementation Open-source Python package with a command line interface (CLI), freely available at https://github.com/almaan/sepal under an MIT licence. A mirror of the GitHub repository can be found at Zenodo, doi: 10.5281/zenodo.4573237. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MBRS-46. CHARTING NEOPLASTIC AND IMMUNE CELL HETEROGENEITY IN HUMAN AND GEM MODELS OF MEDULLOBLASTOMA USING scRNAseq

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii406-iii406
Author(s):  
Andrew Donson ◽  
Kent Riemondy ◽  
Sujatha Venkataraman ◽  
Ahmed Gilani ◽  
Bridget Sanford ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Genetically Engineered ◽  
Cellular Heterogeneity ◽  
Cell Heterogeneity ◽  
Transcriptomic Data ◽  
Single Cell Rna Sequencing ◽  
Transcript Profiles

Abstract We explored cellular heterogeneity in medulloblastoma using single-cell RNA sequencing (scRNAseq), immunohistochemistry and deconvolution of bulk transcriptomic data. Over 45,000 cells from 31 patients from all main subgroups of medulloblastoma (2 WNT, 10 SHH, 9 GP3, 11 GP4 and 1 GP3/4) were clustered using Harmony alignment to identify conserved subpopulations. Each subgroup contained subpopulations exhibiting mitotic, undifferentiated and neuronal differentiated transcript profiles, corroborating other recent medulloblastoma scRNAseq studies. The magnitude of our present study builds on the findings of existing studies, providing further characterization of conserved neoplastic subpopulations, including identification of a photoreceptor-differentiated subpopulation that was predominantly, but not exclusively, found in GP3 medulloblastoma. Deconvolution of MAGIC transcriptomic cohort data showed that neoplastic subpopulations are associated with major and minor subgroup subdivisions, for example, photoreceptor subpopulation cells are more abundant in GP3-alpha. In both GP3 and GP4, higher proportions of undifferentiated subpopulations is associated with shorter survival and conversely, differentiated subpopulation is associated with longer survival. This scRNAseq dataset also afforded unique insights into the immune landscape of medulloblastoma, and revealed an M2-polarized myeloid subpopulation that was restricted to SHH medulloblastoma. Additionally, we performed scRNAseq on 16,000 cells from genetically engineered mouse (GEM) models of GP3 and SHH medulloblastoma. These models showed a level of fidelity with corresponding human subgroup-specific neoplastic and immune subpopulations. Collectively, our findings advance our understanding of the neoplastic and immune landscape of the main medulloblastoma subgroups in both humans and GEM models.

scholarly journals Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jifang Zhang ◽  
Jian Zhao ◽  
Qunyun Tan ◽  
Xiaojun Qiu ◽  
Shiyong Mei
Keyword(s):  
Transcription Factors ◽  
Raphanus Sativus ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Comparative Transcriptome ◽  
Structural Genes ◽  
Key Genes ◽  
Transcript Profiles ◽  
Species Specific ◽  
Anthocyanin Biosynthetic Genes

AbstractRadish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.

scholarly journals Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations

Open Biology ◽  
2012 ◽  
Vol 2 (7) ◽  
pp. 120091 ◽  
Author(s):  
Matthew D. Rolfe ◽  
Andrea Ocone ◽  
Melanie R. Stapleton ◽  
Simon Hall ◽  
Eleanor W. Trotter ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Systems Analysis ◽  
Kinetic Modelling ◽  
Statistical Modelling ◽  
Spatial Effects ◽  
Transcript Profile ◽  
Terminal Oxidases ◽  
Adaptive Processes ◽  
Membrane Bound ◽  
Transcript Profiles

Understanding gene regulation requires knowledge of changes in transcription factor (TF) activities. Simultaneous direct measurement of numerous TF activities is currently impossible. Nevertheless, statistical approaches to infer TF activities have yielded non-trivial and verifiable predictions for individual TFs. Here, global statistical modelling identifies changes in TF activities from transcript profiles of Escherichia coli growing in stable (fixed oxygen availabilities) and dynamic (changing oxygen availability) environments. A core oxygen-responsive TF network, supplemented by additional TFs acting under specific conditions, was identified. The activities of the cytoplasmic oxygen-responsive TF, FNR, and the membrane-bound terminal oxidases implied that, even on the scale of the bacterial cell, spatial effects significantly influence oxygen-sensing. Several transcripts exhibited asymmetrical patterns of abundance in aerobic to anaerobic and anaerobic to aerobic transitions. One of these transcripts, ndh , encodes a major component of the aerobic respiratory chain and is regulated by oxygen-responsive TFs ArcA and FNR. Kinetic modelling indicated that ArcA and FNR behaviour could not explain the ndh transcript profile, leading to the identification of another TF, PdhR, as the source of the asymmetry. Thus, this approach illustrates how systematic examination of regulatory responses in stable and dynamic environments yields new mechanistic insights into adaptive processes.

Gene transcript profiles in the desert plant Nitraria tangutorum during fruit development and ripening

2015 ◽  
Vol 291 (1) ◽  
pp. 383-398
Author(s):  
Jia Wang ◽  
Zhenhua Dang ◽  
Huirong Zhang ◽  
Linlin Zheng ◽  
Tebuqin Borjigin ◽  
...  
Keyword(s):  
Fruit Development ◽  
Desert Plant ◽  
Gene Transcript ◽  
Fruit Development And Ripening ◽  
Nitraria Tangutorum ◽  
Transcript Profiles

Cross-species comparison of hepatic sex differences identified in transcript profiles

2006 ◽  
Vol 3 ◽  
pp. S47
Author(s):  
Louisa Cheung ◽  
Elizabeth Rico-Bautista ◽  
Gunnar Norsted ◽  
Petra Tollet-Egnell
Keyword(s):  
Sex Differences ◽  
Species Comparison ◽  
Transcript Profiles ◽  
Cross Species Comparison

scholarly journals Molecular Characterization of the Transcription Factors in Susceptible Poplar Infected with Virulent Melampsora larici-populina

2019 ◽  
Vol 20 (19) ◽  
pp. 4806 ◽  
Author(s):  
Qiaoli Chen ◽  
Jianan Wang ◽  
Danlei Li ◽  
Zhiying Wang ◽  
Feng Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Calcium Binding ◽  
Bioinformatics Analysis ◽  
Pathological Process ◽  
Compatible Interaction ◽  
Time Points ◽  
Time Periods ◽  
Two Phases ◽  
Transcript Profiles

Transcription factors (TFs) have been shown to play important roles in determining poplar susceptibility. In this study, the transcript profiles of five resistance-related TF groups at different time points were investigated to study the roles of TFs in the compatible interaction between ‘Robusta’ (Populus nigra × P. deltoides) and the virulent E4 race of Melampsora larici-populina. The susceptibility test indicated that the parasitic process of E4 could be divided into two representative time periods: the infection phase and the production phase. Bioinformatics analysis showed that in these two phases, E4 infection induced a network of TFs in ‘Robusta’. Although some TFs responded rapidly and positively, most TFs did not respond to E4, especially during the infection phase. The ethylene, jasmonic acid, and auxin pathways were downregulated, while a calcium-binding protein was upregulated. No other significantly changed phytohormone-related genes were found, which was consistent with the pathological process in the absence of an immune response, suggesting that the lack of response of most TFs during the infection phase of E4 is related to the susceptibility of ‘Robusta’.

Genome-wide screening of altered m6A-tagged transcript profiles in the hippocampus after traumatic brain injury in mice

Epigenomics ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 805-819 ◽  
Author(s):  
Yiqin Wang ◽  
Jian Mao ◽  
Xin Wang ◽  
Yong Lin ◽  
Guoqiang Hou ◽  
...  
Keyword(s):  
Traumatic Brain Injury ◽  
Brain Injury ◽  
Genome Wide ◽  
Transcript Profiles

scholarly journals Comparing regional transcript profiles from maize primary roots under well-watered and low water potential conditions

2006 ◽  
Vol 58 (2) ◽  
pp. 279-289 ◽  
Author(s):  
V Poroyko ◽  
WG Spollen ◽  
LG Hejlek ◽  
AG Hernandez ◽  
ME LeNoble ◽  
...  
Keyword(s):  
Water Potential ◽  
Primary Roots ◽  
Low Water Potential ◽  
Transcript Profiles ◽  
Potential Conditions
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