کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
2058569 1543958 2016 6 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
IsoSeq analysis and functional annotation of the infratentorial ependymoma tumor tissue on PacBio RSII platform
موضوعات مرتبط
علوم زیستی و بیوفناوری بیوشیمی، ژنتیک و زیست شناسی مولکولی بیوشیمی، ژنتیک و زیست شناسی مولکولی (عمومی)
پیش نمایش صفحه اول مقاله
IsoSeq analysis and functional annotation of the infratentorial ependymoma tumor tissue on PacBio RSII platform
چکیده انگلیسی


• Produced 2952 unique protein accessions in the nr protein database
• Identified 307 KEGG-pathways with 442 enzyme-codes for 1172 unique-sequences
• Identified transcript cluster-IDs in Level-2 and -3 GO-terms with alternative splicing index
• Involvement of PNMT, SNN and LAMB1-brain specific genes in Ependymoma

Here, we sequenced and functionally annotated the long reads (1–2 kb) cDNAs library of an infratentorial ependymoma tumor tissue on PacBio RSII by Iso-Seq protocol using SMRT technology. 577 MB, data was generated from the brain tissues of ependymoma tumor patient, producing 1,19,313 high-quality reads assembled into 19,878 contigs using Celera assembler followed by Quiver pipelines, which produced 2952 unique protein accessions in the nr protein database and 307 KEGG pathways.Additionally, when we compared GO terms of second and third level with alternative splicing data obtained through HTA Array2.0. We identified four and twelve transcript cluster IDs in Level-2 and Level-3 scores respectively with alternative splicing index predicting mainly the major pathways of hallmarks of cancer. Out of these transcript cluster IDs only transcript cluster IDs of gene PNMT, SNN and LAMB1 showed Reads Per Kilobase of exon model per Million mapped reads (RPKM) values at gene-level expression (GE) and transcript-level (TE) track. Most importantly, brain-specific genes–—PNMT, SNN and LAMB1 show their involvement in Ependymoma.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Meta Gene - Volume 7, February 2016, Pages 70–75
نویسندگان
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