scholarly journals In silico Analysis of 3'-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

DNA Research ◽  
2011 ◽  
Vol 18 (3) ◽  
pp. 189-200 ◽  
Author(s):  
M. Tanaka ◽  
Y. Sakai ◽  
O. Yamada ◽  
T. Shintani ◽  
K. Gomi
Keyword(s):  
Aspergillus Oryzae ◽  
Expressed Sequence Tags ◽  
In Silico ◽  
In Silico Analysis ◽  
Genomic Sequencing ◽  
Sequencing Data ◽  
Expressed Sequence ◽  
Silico Analysis

Comparative gene-based in silico analysis of transcriptomes in different bovine tissues and (or) organs

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1164-1172 ◽  
Author(s):  
Zhihua Jiang ◽  
Xiao-Lin Wu ◽  
Matthew D Garcia ◽  
Kirsten B Griffin ◽  
Jennifer J Michal ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
In Silico ◽  
Expression Patterns ◽  
In Silico Analysis ◽  
Orthologous Genes ◽  
Functional Relations ◽  
Human Genes ◽  
Expressed Sequence ◽  
Silico Analysis ◽  
Tissue Library

A gene-based approach was used to annotate 322 168 cattle expressed sequence tags (ESTs) based on human genes in order to census the transcriptomes, analyze their expression similarities, and identify genes preferentially expressed in different bovine tissues and (or) organs. Of the 34 157 human coding genes used in a standalone BLAST search, 14 928 could be matched with provisional orthologous sequences in a total of 230 135 bovine ESTs. The remaining 92 033 bovine ESTs were estimated to represent an additional 5970 genes in cattle. On average, ~8600 genes were estimated to be expressed in a single tissue and (or) organ and 13 000 in a pooled tissue library. On the basis of the estimated numbers of genes, no more than 3% of genes would be missed when ~34 000 ESTs were sequenced from a single tissue and (or) organ library and ~40 000 ESTs from a pooled source, respectively. Cluster analyses of the gene expression patterns among 12 single tissues and (or) organs in cattle revealed that their expression similarities would depend on physiological functions. In addition, a total of 1502 genes were identified as preferentially expressed genes in these 12 single tissues and (or) organs with LOD (logarithm of the odds, base 10) ≥ 3.0. Therefore, our study provides some insights for further investigating the developmental and functional relations of various tissues and organs in mammals.Key words: cattle, expressed sequence tags (ESTs), orthologous genes, comparative gene-based approach, in silico census, tissue/organs, transcriptomes.

scholarly journals Discovery in Silico and Characterization in Vitro of Novel Genes Exclusively Expressed in the Mouse Epididymis

2003 ◽  
Vol 17 (11) ◽  
pp. 2138-2151 ◽  
Author(s):  
Jenni Penttinen ◽  
Dwi Ari Pujianto ◽  
Petra Sipilä ◽  
Ilpo Huhtaniemi ◽  
Matti Poutanen
Keyword(s):  
Expressed Sequence Tags ◽  
In Silico ◽  
In Silico Analysis ◽  
Rnase A ◽  
Computational Tools ◽  
Cdna Sequences ◽  
Expressed Sequence ◽  
Silico Analysis ◽  
Mouse Epididymis

Abstract Epididymal proteins interact with sperm during their passage through the epididymis and thus contribute to the maturation and fertilizing capacity of the spermatozoa. In the present study we have discovered five novel epididymis-specific genes through in silico analysis of expressed sequence tags (ESTs) at the UniGene library collection. The strategy used is a powerful way to discover novel epididymis-specific genes. The full-length cDNA sequences were determined, and computational tools were used to characterize the genomic structures and to predict putative functions for the encoded proteins. In vitro analyses revealed that all five genes characterized were highly expressed in the defined areas of the epididymis, and they were not expressed at significant levels in any other tissue. Three of the genes were named on the basis of their putative functions: Spint4 (serine protease inhibitor, Kunitz type 4), and Rnase9 and Rnase10 (ribonuclease, Rnase A family 9 and 10), while for the ESTs AV381130 and AV381126 no putative functions could be predicted. The expression of Spint4, Rnase9, and AV381130 was found to be under a direct or indirect regulation by androgens, while the expression of Rnase10 is regulated by a testicular factor(s) other than androgen. None of the genes were expressed in the immature epididymis, while mRNAs were detected from d 17 onward, at the time of maturation of epididymal epithelium. However, the expression of AV381130 was not detected until d 30 after birth, indicating a close connection between gene expression and puberty.

In Silico Analysis of Micro-RNA Sequencing Data

2021 ◽  
pp. 231-251
Author(s):  
Ernesto Aparicio-Puerta ◽  
Bastian Fromm ◽  
Michael Hackenberg ◽  
Marc K. Halushka
Keyword(s):  
Rna Sequencing ◽  
In Silico ◽  
In Silico Analysis ◽  
Micro Rna ◽  
Sequencing Data ◽  
Silico Analysis

scholarly journals The pattern of gene copy number alteration (CNAs) in hepatocellular carcinoma: an in silico analysis

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Arman Shahrisa ◽  
Maryam Tahmasebi-Birgani ◽  
Hossein Ansari ◽  
Zahra Mohammadi ◽  
Vinicio Carloni ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
In Silico ◽  
Copy Number ◽  
Copy Number Alteration ◽  
Gene Copy Number ◽  
In Silico Analysis ◽  
Gene Copy ◽  
Sequencing Data ◽  
Silico Analysis

Abstract Background Hepatocellular carcinoma (HCC) is the most common type of liver cancer that occurs predominantly in patients with previous liver conditions. In the absence of an ideal screening modality, HCC is usually diagnosed at an advanced stage. Recent studies show that loss or gain of genomic materials can activate the oncogenes or inactivate the tumor suppressor genes to predispose cells toward carcinogenesis. Here, we evaluated both the copy number alteration (CNA) and RNA sequencing data of 361 HCC samples in order to locate the frequently altered chromosomal regions and identify the affected genes. Results Our data show that the chr1q and chr8p are two hotspot regions for genomic amplifications and deletions respectively. Among the amplified genes, YY1AP1 (chr1q22) possessed the largest correlation between CNA and gene expression. Moreover, it showed a positive correlation between CNA and tumor grade. Regarding deleted genes, CHMP7 (chr8p21.3) possessed the largest correlation between CNA and gene expression. Protein products of both genes interact with other cellular proteins to carry out various functional roles. These include ASH1L, ZNF496, YY1, ZMYM4, CHMP4A, CHMP5, CHMP2A and CHMP3, some of which are well-known cancer-related genes. Conclusions Our in-silico analysis demonstrates the importance of copy number alterations in the pathology of HCC. These findings open a door for future studies that evaluate our results by performing additional experiments.

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