Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: Maximum entropy estimates of splice junction strengths

2003 ◽  
Vol 23 (1) ◽  
pp. 67-76 ◽  
Author(s):  
Laura Eng ◽  
Gabriela Coutinho ◽  
Shareef Nahas ◽  
Gene Yeo ◽  
Robert Tanouye ◽  
...  
Keyword(s):  
Maximum Entropy ◽  
Splice Junction ◽  
Noncoding Regions ◽  
Splicing Mutations ◽  
Atm Gene ◽  
Entropy Estimates

scholarly journals Pan-cancer repository of validated natural and cryptic mRNA splicing mutations

F1000Research ◽  
2019 ◽  
Vol 7 ◽  
pp. 1908 ◽  
Author(s):  
Ben C. Shirley ◽  
Eliseos J. Mucaki ◽  
Peter K. Rogan
Keyword(s):  
Splice Junction ◽  
Cancer Genome ◽  
Mrna Splicing ◽  
The Cancer Genome Atlas ◽  
Splice Sites ◽  
Global Alliance ◽  
Multiple Tumor ◽  
Link Type ◽  
Splicing Mutations ◽  
Single Nucleotide Polymorphism Database

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 341,486 of these validated mutations, the majority of which (69.9%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 131,347 unique mutations which weaken or abolish natural splice sites, and 222,071 mutations which strengthen cryptic splice sites (11,932 affect both simultaneously). 28,812 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon “Validated Splicing Mutations” either separately or in aggregate alongside other Beacons through the public Beacon Network, as well as through our website.

scholarly journals Ataxia-Telangiectasia with Novel Splicing Mutations in the ATM Gene

2014 ◽  
Vol 34 (1) ◽  
pp. 80-84 ◽  
Author(s):  
Heejeong Jeong ◽  
Hee Jae Huh ◽  
Jinyoung Youn ◽  
Ji Sun Kim ◽  
Jin Whan Cho ◽  
...  
Keyword(s):  
Ataxia Telangiectasia ◽  
Splicing Mutations ◽  
Atm Gene

scholarly journals Pan-cancer repository of validated natural and cryptic mRNA splicing mutations

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1908 ◽  
Author(s):  
Ben C. Shirley ◽  
Eliseos J. Mucaki ◽  
Peter K. Rogan
Keyword(s):  
Splice Junction ◽  
Mrna Splicing ◽  
The Cancer Genome Atlas ◽  
Splice Sites ◽  
Global Alliance ◽  
Multiple Tumor ◽  
Link Type ◽  
Splicing Mutations ◽  
Public Resource ◽  
Single Nucleotide Polymorphism Database

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 351,423 of these validated mutations, the majority of which (69.1%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 117,951 unique mutations which weaken or abolish natural splice sites, and 244,415 mutations which strengthen cryptic splice sites (10,943 affect both simultaneously). 27,803 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon “Validated Splicing Mutations” either separately or in aggregate alongside other Beacons through the public Beacon Network (http://www.beacon-network.org/#/search?beacon=cytognomix), as well as through our website (https://validsplicemut.cytognomix.com/).

scholarly journals Common Spectral Features in the 5500-Year Record of Total Carbonate in Sea Sediments and Radiocarbon in Tree Rings

Radiocarbon ◽  
1992 ◽  
Vol 34 (3) ◽  
pp. 798-805 ◽  
Author(s):  
Giuliana Cini Castagnoli ◽  
Giuseppe Bonino ◽  
Marina Serio ◽  
Charles P. Sonett
Keyword(s):  
Maximum Entropy ◽  
Tree Rings ◽  
Spectral Features ◽  
Ionian Sea ◽  
Total Carbonate ◽  
Sea Bottom ◽  
Time Record ◽  
Climatic Record ◽  
Entropy Estimates

We analyze here the time record of total carbonate carried as CaCO3 in a sea-bottom core from the Ionian Sea. Several major periods appear, most strongly at 1100, 690, 500, 340, 250 and 90 yr, confirmed both in the periodogram and maximum entropy estimates. The Gleissberg period appears in common with the 14C and other records, such as the sunspot index and aurorae. The manifestation of this period in what we surmise to be a climatic record is further evidence that the Gleissberg period has correlated bolometric and electrodynamic aspects.

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