scholarly journals TimeMeter assesses temporal gene expression similarity and identifies differentially progressing genes

2020 ◽  
Vol 48 (9) ◽  
pp. e51-e51
Author(s):  
Peng Jiang ◽  
Connie S Chamberlain ◽  
Ray Vanderby ◽  
James A Thomson ◽  
Ron Stewart
Keyword(s):  
Gene Expression ◽  
Purifying Selection ◽  
Temporal Patterns ◽  
Cancer Prognosis ◽  
Temporal Gene Expression ◽  
Pattern Similarity ◽  
Developmental Divergence ◽  
Early Developmental ◽  
Human And Mouse ◽  
Study Development

Abstract Comparative time series transcriptome analysis is a powerful tool to study development, evolution, aging, disease progression and cancer prognosis. We develop TimeMeter, a statistical method and tool to assess temporal gene expression similarity, and identify differentially progressing genes where one pattern is more temporally advanced than the other. We apply TimeMeter to several datasets, and show that TimeMeter is capable of characterizing complicated temporal gene expression associations. Interestingly, we find: (i) the measurement of differential progression provides a novel feature in addition to pattern similarity that can characterize early developmental divergence between two species; (ii) genes exhibiting similar temporal patterns between human and mouse during neural differentiation are under strong negative (purifying) selection during evolution; (iii) analysis of genes with similar temporal patterns in mouse digit regeneration and axolotl blastema differentiation reveals common gene groups for appendage regeneration with potential implications in regenerative medicine.

scholarly journals Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

2021 ◽  
Vol 22 (12) ◽  
pp. 6556
Author(s):  
Junjun Huang ◽  
Xiaoyu Li ◽  
Xin Chen ◽  
Yaru Guo ◽  
Weihong Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abc Transporters ◽  
Developmental Stages ◽  
Aluminum Toxicity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Purifying Selection ◽  
Biotic Stresses ◽  
Genome Wide ◽  
New Germplasm

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.

Temporal gene expression profiling of maslinic acid-treated Raji cells

2021 ◽  
Author(s):  
Wai Meng Lau ◽  
Menaga Subramaniam ◽  
Hoe Han Goh ◽  
Yang Mooi Lim
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Raji Cells ◽  
Maslinic Acid ◽  
Temporal Gene Expression ◽  
Key Pathways

An hourly progression of gene expression profiling in maslinic acid treated Raji cells, which reported activation of several key pathways.

scholarly journals Microarray Analyses of Gene Expression during Chondrocyte Differentiation Identifies Novel Regulators of Hypertrophy

2005 ◽  
Vol 16 (11) ◽  
pp. 5316-5333 ◽  
Author(s):  
Claudine G. James ◽  
C. Thomas G. Appleton ◽  
Veronica Ulici ◽  
T. Michael Underhill ◽  
Frank Beier
Keyword(s):  
Gene Expression ◽  
Bone Development ◽  
Skeletal Development ◽  
Expression Patterns ◽  
Chondrocyte Differentiation ◽  
Endochondral Bone ◽  
Temporal Gene Expression ◽  
Affymetrix Microarrays ◽  
Time Period ◽  
And Cluster Analysis

Ordered chondrocyte differentiation and maturation is required for normal skeletal development, but the intracellular pathways regulating this process remain largely unclear. We used Affymetrix microarrays to examine temporal gene expression patterns during chondrogenic differentiation in a mouse micromass culture system. Robust normalization of the data identified 3300 differentially expressed probe sets, which corresponds to 1772, 481, and 249 probe sets exhibiting minimum 2-, 5-, and 10-fold changes over the time period, respectively. GeneOntology annotations for molecular function show changes in the expression of molecules involved in transcriptional regulation and signal transduction among others. The expression of identified markers was confirmed by RT-PCR, and cluster analysis revealed groups of coexpressed transcripts. One gene that was up-regulated at later stages of chondrocyte differentiation was Rgs2. Overexpression of Rgs2 in the chondrogenic cell line ATDC5 resulted in accelerated hypertrophic differentiation, thus providing functional validation of microarray data. Collectively, these analyses provide novel information on the temporal expression of molecules regulating endochondral bone development.

scholarly journals TriGen: A genetic algorithm to mine triclusters in temporal gene expression data

2014 ◽  
Vol 132 ◽  
pp. 42-53 ◽  
Author(s):  
D. Gutiérrez-Avilés ◽  
C. Rubio-Escudero ◽  
F. Martínez-Álvarez ◽  
J.C. Riquelme
Keyword(s):  
Gene Expression ◽  
Genetic Algorithm ◽  
Gene Expression Data ◽  
Expression Data ◽  
Temporal Gene Expression

scholarly journals Impact of male trait exaggeration on sex-biased gene expression and genome architecture in a water strider

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
William Toubiana ◽  
David Armisén ◽  
Corentin Dechaud ◽  
Roberto Arbore ◽  
Abderrahman Khila
Keyword(s):  
Gene Expression ◽  
Sexual Selection ◽  
Enrichment Analysis ◽  
Purifying Selection ◽  
Genome Architecture ◽  
Water Strider ◽  
Secondary Sexual Traits ◽  
Genomic Regions ◽  
Small Clusters ◽  
Secondary Sexual

Abstract Background Exaggerated secondary sexual traits are widespread in nature and often evolve under strong directional sexual selection. Although heavily studied from both theoretical and empirical viewpoints, we have little understanding of how sexual selection influences sex-biased gene regulation during the development of exaggerated secondary sexual phenotypes, and how these changes are reflected in genomic architecture. This is primarily due to the limited availability of representative genomes and associated tissue and sex transcriptomes to study the development of these traits. Here we present the genome and developmental transcriptomes, focused on the legs, of the water strider Microvelia longipes, a species where males exhibit strikingly long third legs compared to females, which they use as weapons. Results We generated a high-quality genome assembly with 90% of the sequence captured in 13 scaffolds. The most exaggerated legs in males were particularly enriched in both sex-biased and leg-biased genes, indicating a specific signature of gene expression in association with trait exaggeration. We also found that male-biased genes showed patterns of fast evolution compared to non-biased and female-biased genes, indicative of directional or relaxed purifying selection. By contrast to male-biased genes, female-biased genes that are expressed in the third legs, but not the other legs, are over-represented in the X chromosome compared to the autosomes. An enrichment analysis for sex-biased genes along the chromosomes revealed also that they arrange in large genomic regions or in small clusters of two to four consecutive genes. The number and expression of these enriched regions were often associated with the exaggerated legs of males, suggesting a pattern of common regulation through genomic proximity in association with trait exaggeration. Conclusion Our findings indicate how directional sexual selection may drive sex-biased gene expression and genome architecture along the path to trait exaggeration and sexual dimorphism.

scholarly journals Clinicopathologic and gene expression parameters predict liver cancer prognosis

BMC Cancer ◽  
2011 ◽  
Vol 11 (1) ◽  
Author(s):  
Ke Hao ◽  
John Lamb ◽  
Chunsheng Zhang ◽  
Tao Xie ◽  
Kai Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Cancer ◽  
Cancer Prognosis
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