Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The exploration of Missing Proteins by a combination approach to enrich the low abundance membrane proteins from several cancer cell lines

ABSTRACT: Our goal is the identification of more and more the missing proteins from cancer cell lines. This project focuses on the membrance proteins separated by the ultracentrifuge and the low abundant peptides enriched by the Proteominer Kit and the hydrophobic peptides extracted by the organic solvent Acetonitrile.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Colon Cancer,Cervix Carcinoma

SUBMITTER: yuanliang zhang

LAB HEAD: Siqi Liu

PROVIDER: PXD014058 | Pride | 2019-12-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20181120_HCT116_PACN.pep.xml	Pepxml
	20181120_HCT116_PACN_down_1.raw	Raw
	20181120_HCT116_PACN_down_10.raw	Raw
	20181120_HCT116_PACN_down_11.raw	Raw
	20181120_HCT116_PACN_down_12.raw	Raw

Items per page:

1 - 5 of 329

Publications

Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines.

Zhang Yuanliang Y Lin Zhilong Z Tan Yifan Y Bu Fanyu F Hao Piliang P Zhang Keren K Yang Huanming H Liu Siqi S Ren Yan Y

Journal of proteome research 20191210 1

The mission of the Chromosome-Centric Human Proteome Project (C-HPP) to discover missing proteins (MPs) has become increasingly difficult due to the remaining low-abundance, high-hydrophobicity, or low-molecular-weight MPs. We have reported two approaches to resolve these identification problems for the low-abundance and high-hydrophobicity MPs, respectively. In this study, to improve the identification of low-abundance MPs with high hydrophobicity, we combined two approaches and obtained MPs fr ...[more]

PMID: 31773964

Similar Datasets

The exploration of Missing Proteins by a combination approach to enrich the low abundance membrane proteins from several cancer cell lines

Project description:Our goal is the identification of more and more the missing proteins from cancer cell lines. This project focuses on the membrance proteins separated by the ultracentrifuge and the low abundant peptides enriched by the Proteominer Kit and the hydrophobic peptides extracted by the organic solvent Acetonitrile.

2020-10-26 | MSV000086369 | MassIVE

D283 MED, a cell line derived from peritoneal metastatic medulloblastoma — a good choice for missing protein discovery

Project description:Our goal is the identification of more and more missing proteins from cancer cell lines. This project focuses on D283 med and U-118mg cell lines which contribute to 12 missing protein identification.

2020-11-26 | PXD021482 | Pride

Spatial Proteomics for Further Exploration of Missing Proteins: A Case Study of the Ovary.

Project description:In the quest for "missing proteins" (MPs), the proteins encoded by the human genome still lacking evidence of existence at the protein level, novel approaches are needed to detect this challenging group of proteins. The current count stands at 1,343 MPs, and it is likely that many of these proteins are expressed at low levels, in rare cell or tissue types, or the cells in which they are expressed may only represent a small minority of the tissue. Here, we used an integrated omics approach to identify and explore MPs in human ovaries. By taking advantage of publicly available transcriptomics and antibody-based proteomics data in the Human Protein Atlas (HPA), we selected 18 candidates for further immunohistochemical analysis using an exclusive collection of ovarian tissues from women and patients of reproductive age. The results were compared with data from single-cell mRNA sequencing, and seven proteins (CTXN1, MRO, RERGL, TTLL3, TRIM61, TRIM73, and ZNF793) could be validated at the single-cell type level with both methods. We present for the first time the cell type-specific spatial localization of 18 MPs in human ovarian follicles, thereby showcasing the utility of the HPA database as an important resource for identification of MPs suitable for exploration in specialized tissue samples. The results constitute a starting point for further quantitative and qualitative analysis of the human ovaries, and the novel data for the seven proteins that were validated with both methods should be considered as evidence of existence of these proteins in human ovary.

| S-EPMC10088045 | biostudies-literature

Finding missing proteins from epigenetically manipulated human cells

Project description:We performed transcriptome sequencing to assess the genes turn on in the cell under epigenetically manipulation. MHCC97H, A549 and HCT116 were treated by GSK126, S2101 and TSA respectively. We detected the missing proteins in the cells under epigenetically manipulation.

2016-05-23 | GSE69420 | GEO

Genome-wide exploration of the GDSL-type esterase/lipase gene family in rapeseed reveals several <i>BnGELP</i> proteins active during early seedling development.

Project description:The Gly-Asp-Ser-Leu (GDSL)-type esterase/lipase proteins (GELP) are one of the most important families of lipolytic enzymes and play prominent roles in seed germination and early seedling establishment through mobilizing the lipids stored in seeds. However, there are no comprehensive studies systematically investigating the GELP gene family in Brassica napus (BnGELP), and their biological significance to these physiological processes are far from understood. In the present study, a total of 240 BnGELP genes were identified in B. napus cultivar "Zhongshuang 11" (ZS11), which is nearly 2.3-fold more GELP genes than in Arabidopsis thaliana. The BnGELP genes clustered into 5 clades based on phylogenetic analysis. Ten BnGELPs were identified through zymogram analysis of esterase activity followed by mass spectrometry, among which five clustered into the clade 5. Gene and protein architecture, gene expression, and cis-element analyses of BnGELP genes in clade 5 suggested that they may play different roles in different tissues and in response to different abiotic stresses. BnGELP99 and BnGELP159 were slightly induced by cold, which may be attributed to two low-temperature responsive cis-acting regulatory elements present in their promoters. An increased activity of esterase isozymes by cold was also observed, which may reflect other cold inducible esterases/lipases in addition to the ten identified BnGELPs. This study provides a systemic view of the BnGELP gene family and offers a strategy for researchers to identify candidate esterase/lipase genes responsible for lipid mobilization during seed germination and early seedling establishment.

| S-EPMC10050346 | biostudies-literature

Exploration of the lipid-regulating effects of Rosa roxburghii flavonoids in hyperlipidemic mice

Project description:Hyperlipidemia (HLP), an insidious threat to human health in modern society, can deteriorate and lead to various other metabolic diseases. This study focuses on transcriptomic analysis of liver samples from C57BL/6 mice, which were divided into the following groups: control group (C), hyperlipidemia model group (M), and three groups treated with flavonoids from Rosa roxburghii—quercetin at 200 mg/kg (QU), myricetin at 75 mg/kg (MY), and kaempferol at 100 mg/kg (KA). Except for the control group, all other groups were maintained on a high-fat diet for 6 weeks. To investigate the commonalities among the three flavonoid components from Rosa roxburghii, differentially expressed genes (DEGs) between each treatment group and the model group were screened to identify common expression genes.

2024-07-12 | GSE271599 | GEO

Electronic medical records and genomics (eMERGE) network exploration in cataract: several new potential susceptibility loci.

Project description:Cataract is the leading cause of blindness in the world, and in the United States accounts for approximately 60% of Medicare costs related to vision. The purpose of this study was to identify genetic markers for age-related cataract through a genome-wide association study (GWAS).In the electronic medical records and genomics (eMERGE) network, we ran an electronic phenotyping algorithm on individuals in each of five sites with electronic medical records linked to DNA biobanks. We performed a GWAS using 530,101 SNPs from the Illumina 660W-Quad in a total of 7,397 individuals (5,503 cases and 1,894 controls). We also performed an age-at-diagnosis case-only analysis.We identified several statistically significant associations with age-related cataract (45 SNPs) as well as age at diagnosis (44 SNPs). The 45 SNPs associated with cataract at p<1×10(-5) are in several interesting genes, including ALDOB, MAP3K1, and MEF2C. All have potential biologic relationships with cataracts.This is the first genome-wide association study of age-related cataract, and several regions of interest have been identified. The eMERGE network has pioneered the exploration of genomic associations in biobanks linked to electronic health records, and this study is another example of the utility of such resources. Explorations of age-related cataract including validation and replication of the association results identified herein are needed in future studies.

| S-EPMC4168835 | biostudies-literature

Differential transcription network analysis for Fusarium head blight disease of barley in combination with drought stress

Project description:For improvement of stress and disease resistance of barley, this global transcriptomic study focuses on how drought conditions affect Fusarium head blight (FHB) severity in spring barley. In general, drought-stress prior to Fusarium culmorum infection reduced FHB-susceptibility. This study gives evidence, that FHB-severity and strength of drought responses is variety-dependent under complex stress situations.

2023-09-15 | GSE223521 | GEO

Relative quantification of several plasma proteins during liver transplantation surgery.

Project description:Plasma proteome is widely used in studying changes occurring in human body during disease or other disturbances. Immunological methods are commonly used in such studies. In recent years, mass spectrometry has gained popularity in high-throughput analysis of plasma proteins. In this study, we tested whether mass spectrometry and iTRAQ-based protein quantification might be used in proteomic analysis of human plasma during liver transplantation surgery to characterize changes in protein abundances occurring during early graft reperfusion. We sampled blood from systemic circulation as well as blood entering and exiting the liver. After immunodepletion of six high-abundant plasma proteins, trypsin digestion, iTRAQ labeling, and cation-exchange fractionation, the peptides were analyzed by reverse phase nano-LC-MS/MS. In total, 72 proteins were identified of which 31 could be quantified in all patient specimens collected. Of these 31 proteins, ten, mostly medium-to-high abundance plasma proteins with a concentration range of 50-2000?mg/L, displayed relative abundance change of more than 10%. The changes in protein abundance observed in this study allow further research on the role of several proteins in ischemia-reperfusion injury during liver transplantation and possibly in other surgery.

| S-EPMC3237013 | biostudies-literature

Novel miR-b2122 regulates several ALS-related RNA-binding proteins.

Project description:Common pathological features of amyotrophic lateral sclerosis (ALS) include cytoplasmic aggregation of several RNA-binding proteins. Out of these RNA-binding proteins, TDP-43, FUS/TLS and RGNEF have been shown to co-aggregate with one another within motor neurons of sporadic ALS (sALS) patients, suggesting that there may be a common regulatory network disrupted. MiRNAs have been a recent focus in ALS research as they have been identified to be globally down-regulated in the spinal cord of ALS patients. The objective of this study was to identify if there are miRNA(s) dysregulated in sALS that are responsible for regulating the TDP-43, FUS/TLS and RGNEF network. In this study, we identify miR-194 and miR-b2122 to be significantly down-regulated in sALS patients, and were predicted to regulate TARDBP, FUS/TLS and RGNEF expression. Reporter gene assays and RT-qPCR revealed that miR-b2122 down-regulates the reporter gene through direct interactions with either the TARDBP, FUS/TLS, or RGNEF 3'UTR, while miR-194 down-regulates firefly expression when it contained either the TARDBP or FUS/TLS 3'UTR. Further, we showed that miR-b2122 regulates endogenous expression of all three of these genes in a neuronal-derived cell line. Also, an ALS-associated mutation in the FUS/TLS 3'UTR ablates the ability of miR-b2122 to regulate reporter gene linked to FUS/TLS 3'UTR, and sALS samples which showed a down-regulation in miR-b2122 also showed an increase in FUS/TLS protein expression. Overall, we have identified a novel miRNA that is down-regulated in sALS that appears to be a central regulator of disease-related RNA-binding proteins, and thus its dysregulation likely contributes to TDP-43, FUS/TLS and RGNEF pathogenesis in sALS.

| S-EPMC5625648 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data