Computational protocol: Ets-2 Regulates Cell Apoptosis via the Akt Pathway, through the Regulation of Urothelial Cancer Associated 1, a Long Non-Coding RNA, in Bladder Cancer Cells

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Protocol publication

[…] Previously, the full length of the UCA1 cDNA and its transcriptional start site (TSS) were identified using SMART RACE technology . In this study, MegaBLAST (NCBI) program was used to map the UCA1 gene and its 5′ flanking region and DNA sequences were downloaded from GenBank (NC_000019.9). The TSS of the UCA1 gene was marked as +1. To predict the promoter and putative transcription factors, the following some online software were utilized. The promoter and TSS predict tools include the FPROM program from Softberry software (http://linux1.softberry.com/berry.phtml?topic=fprom&group=programs&subgroup=promoter) and PromoterInspector program from genomatix (http://www.genomatix.de/online_help/help_gems/PromoterInspector_help.html) . The MatInspector program from genomatix (http://www.genomatix.de/online_help/help_matinspector/matinspector_help.html) , was used for the transcription factor prediction. […]

Pipeline specifications

Software tools BLASTN, FPROM, PromoterInspector, MatInspector
Databases Online Help
Application Genome annotation
Organisms Homo sapiens
Diseases Urinary Bladder Neoplasms, Neoplasms