PXD002465 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | A novel protein coding potential of long intergenic non-coding RNAs (lincRNAs) in the kinetoplastid protozoan parasite Leishmania major |
Description | Leishmania major is a kinetoplastid protozoan parasite which causes the debilitating infectious disease cutaneous leishmaniasis (CL). This disease results in scars and disfiguration of the infected individuals. The L. major genome was the first leishmanial genome to be sequenced in 2005 and this study resulted in the identification of 8,300 protein coding genes. This landmark study paved the way for further sequencing of other leishmanial parasites (L. infantum, L. braziliensis and L. donovani). A recent study provided the glimpse of the global transcriptome of L. major promastigotes. This study identified 1,884 uniquely expressed non-coding RNAs (ncRNA) in L. major. Additionally, we had previously mapped the global proteome of L. major promastigote using a proteogenomic approach which resulted in identification of 3,613 proteins in L. major promastigotes which covered 43% of its proteome. In the present study, we have carried out extensive analysis of the 1,884 novel ncRNAs using a proteogenomic approach to identify their protein coding potential. Our analysis resulted in identification of 10 novel protein coding genes based on peptide data and additional hundreds of proteins coding genes based on homology searches of previously classified ncRNA genes. We have analyzed each of these novel protein coding genes and in the process have improved the genome annotation of L. major on the basis of mass spectrometry derived peptide data and also based on homology. |
HostingRepository | PRIDE |
AnnounceDate | 2019-02-12 |
AnnouncementXML | Submission_2019-02-12_07:53:49.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Akhilesh Pandey |
SpeciesList | scientific name: Leishmania major; NCBI TaxID: 5664; |
ModificationList | monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue |
Instrument | LTQ Orbitrap Velos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-07-02 00:41:14 | ID requested | |
1 | 2016-05-11 07:20:01 | announced | |
⏵ 2 | 2019-02-12 07:53:51 | announced | Updated publication reference for PubMed record(s): 27988178. |
Publication List
Pawar H, Pai K, Patole MS, A novel protein coding potential of long intergenic non-coding RNAs (lincRNAs) in the kinetoplastid protozoan parasite Leishmania major. Acta Trop, 167():21-25(2017) [pubmed] |
Keyword List
curator keyword: Biological |
submitter keyword: Cutaneous leishmaniasis, proteomics, gene annotations, non-coding RNA, protozoan parasite |
Contact List
Akhilesh Pandey |
contact affiliation | McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 USA |
contact email | pandey@jhmi.edu |
lab head | |
Akhilesh Pandey |
contact affiliation | Johns Hopkins University |
contact email | pandey@jhmi.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002465
- Label: PRIDE project
- Name: A novel protein coding potential of long intergenic non-coding RNAs (lincRNAs) in the kinetoplastid protozoan parasite Leishmania major