Browse
Submit Data
Databases
API
Help

Dataset Information

551 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human thyroid neoplasms LC-MS/MS analysis

ABSTRACT: The study aimes to evaluate the neoplasm proteomic changes in benign follicular adenoma versus malignant follicular variant of papillary thyroid carcinoma. Tumor and non-tumor adjacent samples were analyzed by liquid nano-chromatography mass spectrometry and protein abundance was evaluated by label free quantification.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Thyroid Gland

DISEASE(S): Papillary Follicular Thyroid Adenocarcinoma,Follicular Adenoma,Disease Free

SUBMITTER: Felicia Antohe

LAB HEAD: Felicia Antohe

PROVIDER: PXD004322 | Pride | 2016-08-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	10ABC_tesut_tiroida16t.prot.xml	Xml
	10ABC_tesut_tiroida91nt.prot.xml	Xml
	10A_B_C_tesut_tiroida50t.prot.xml	Xml
	10A_tesut_tiroida16t.mgf	Mgf
	10A_tesut_tiroida16t.msf	Msf

Items per page:

1 - 5 of 446

Publications

Endoplasmic Reticulum Chaperones Are Potential Active Factors in Thyroid Tumorigenesis.

Uyy Elena E Suica Viorel I VI Boteanu Raluca M RM Manda Dana D Baciu Ancuta E AE Badiu Corin C Antohe Felicia F

Journal of proteome research 20160816 9

The study aimed to evaluate the proteomic changes in benign follicular adenoma versus malignant follicular variant of papillary thyroid carcinoma. Tumor and nontumor adjacent samples were analyzed by liquid nanochromatography mass spectrometry, and protein abundance was evaluated by label-free quantification. Western blotting and quantitative real-time polymerase chain reaction were used to validate and complement the mass spectrometry data. The results demonstrated deregulated expression of fou ...[more]

PMID: 27480176

Similar Datasets

A comprehensive mass spectral library for human thyroid tissues

Project description:Thyroid nodules occur in about 60% of the population. Current diagnostic strategies, however, often fail at distinguishing malignant nodules before surgery, thus leading to unnecessary, invasive treatments. As proteins are involved in all physio/pathological processes, a proteome investigation of biopsied nodules may help correctly classify and identify malignant nodules and discover therapeutic targets. Quantitative mass spectrometry data-independent acquisition (DIA) enables highly reproducible and rapid throughput investigation of proteomes. An exhaustive spectral library of thyroid nodules is essential for DIA yet still unavailable. This study presents a comprehensive thyroid spectral library covering five types of thyroid tissue: multinodular goiter, follicular adenoma, follicular and papillary thyroid carcinoma, and normal thyroid tissue. Our library includes 925,330 transition groups, 157,548 peptide precursors, 121,960 peptides, 9941 protein groups, and 9826 proteins from proteotypic peptides. This library resource was evaluated using three papillary thyroid carcinoma samples and their corresponding adjacent normal thyroid tissue, leading to effective quantification of up to 7863 proteins from biopsy-level thyroid tissues.

2022-05-20 | PXD026395 | Pride

Epigenetic profiling of Follicular thyroid adenomas and carcinomas using high content DNA methylation arrays

Project description:While thyroid nodules per se are frequent (4%–50%), thyroid cancer is rare (∼5% of all thyroid nodules). The minimally invasive Fine Needle Aspiration Cytology (FNAC) is the current gold standard for the diagnosis thyroid nodule malignancy. However, proper discrimination of follicular neoplasias often require more invasive diagnostic techniques. To develop a novel molecular classification system for thyroid cancer malignancy, we performed a genome-wide epigenetic profiling of 54 fresh frozen Follicular like thyroid samples using the Illumina Human DNA Methylation EPIC platform.

2022-09-01 | E-MTAB-10906 | biostudies-arrayexpress

Proteomics of thyroid tumours - Proteomics of thyroid tumours provides new insights into their molecular composition and changes associated with malignancy

Project description:Although most thyroid tumours are benign, thyroid cancer represents the most common malignancy of the endocrine system, comprising mainly follicular and papillary thyroid carcinomas (FTC and PTC, respectively). Previous studies have shed some light on the molecular pathogenesis of thyroid cancer but there have not been any comprehensive mass spectrometry-based proteomic studies to reveal protein expression differences between thyroid tumours and the molecular alterations associated with tumour malignancy. We applied a label-free quantitative mass spectrometry analysis to compare normal thyroid tissue with the three most common tumours of the thyroid gland: follicular adenoma, follicular carcinoma and papillary carcinoma.

2017-05-03 | PXD002732 | Pride

miRNA expression in Follicular Thyroid Adenomas and Carcinoma

Project description:The experiment was performed to identify differentially expressed microRNAs in follicular thyroid carcinoma and adenoma vs. normal thyroid tissue to explore possible common features in the proliferation stages. Furthermore comparisons between the carcinoma and adenoma were performed to search for distinct microRNAs that could be used in a classification model.

2011-11-30 | E-MTAB-736 | biostudies-arrayexpress

Proteotypic differences of follicular-patterned thyroid neoplasms

Project description:The diagnosis of follicular-patterned thyroid tumors such as follicular adenoma (FA), follicular thyroid carcinoma (FTC), and follicular variant of papillary thyroid carcinoma (FvPTC) remains challenging. This study aimed to explore the molecular differences among these three thyroid tumors by proteomic analysis.

2022-09-07 | PXD036553 |

Comprehensive proteomics analysis to distinguish follicular adenoma and follicular thyroid carcinoma from indeterminate thyroid nodules.Comprehensive proteomics analysis to distinguish follicular adenoma and follicular thyroid carcinoma from indeterminate thyroid nodules

Project description:In this study, a total of 202 formalin fixed paraffin embedded (FFPE) thyroid tissues including 62 of benign nodules, 72 of follicular adenoma, and 68 of follicular thyroid carcinoma were used for the analyses. Here, through global FFPE proteomic analysis, proteins differentially expressed by group were identified and quantitative analysis was performed by LC-MS/MS.

2025-10-13 | PXD043154 | Pride

Transcription profiling of micro-RNA genes in human papillary thyroid carcinoma

Project description:We show that numerous miRNAs are transcriptionally up-regulated in papillary thyroid carcinoma (PTC) tumors compared with unaffected thyroid tissue. Among the predicted target genes of the three most upregulated miRNAs (miRs 221, 222 and 146b), only less than 15% showed significant downexpression in transcript level between tumor and unaffected tissue. The KIT gene which is known to be downregulated by miRNAs 221 and 222 displayed dramatic loss of transcript and protein in those tumors that had abundant mir-221, mir-222, and mir-146b transcript. Experiment Overall Design: Total RNA was extracted from paired tumor and normal thyroid tissues from 9 PTC patients. The same set samples were applied to Custom miRNA microarray chips (OSU_CCC version 2.0) and Affymetrix HG-U133 plus 2 chips.

2007-09-01 | E-GEOD-3467 | biostudies-arrayexpress

Human rectal adenoma (8 cases) vs. rectal carcinoma (8 cases)

Project description:Genomic profiling of human rectal adenoma and carcinoma by array-based comparative genomic hybridization Two group experiment, rectal adenoma vs. rectal carcinoma. Biological replicates: 8 adenomas vs. 8 carcinomas

2011-12-20 | E-GEOD-34472 | biostudies-arrayexpress

Multiomic approaches for thyroid cancer diagnosis

Project description:Thyroid cancer is a common endocrine malignancy; however, its diagnosis is not straightforward. The current gold standard for diagnosing thyroid cancer is fine needle aspiration biopsy (FNAB), but when cytological analysis does not provide viable results or samples belong to less defined categories of diagnosis, patients are often referred to diagnostic surgery. Given that not all these nodules require removal, nor all of them are malignant, patients would not necessarily require surgery had the initial FNAB diagnosis been more conclusive. There is therefore a lack of reliable and specific biomarkers for thyroid cancer malignancy, that can complement and improve the current diagnosing methods. “Omics” approaches have gained much attention in the last decade in the field of biomarker discovery for diagnostic and prognostic characterization of various pathophysiological conditions. In this project, proteomics and metabolomics approaches were applied to the same thyroid nodules from patients with benign and malignant lesions. Tissue analysis provided several interesting biomarkers by both proteomics and metabolomics. The combination of these results demonstrated the high energetic and biomass demand of cancer cells, as well as a biomarker panel including 2 free peptides and 2 proteins with high sensitivity and specificity. Together, these results have contributed to increasing the knowledge of thyroid cancer phenotype and corresponding biochemical profiles, as well as providing potential biomarkers for malignancy, and improving diagnostic methodologies.

2023-10-24 | PXD035583 | Pride

Whole-exome sequencing (WES) to assess genomic concordance between an adenoma/adenocarcinoma colonoid culture 14-881 and the source patient tissue

Project description:A patient-derived epithelium-only colon rectal organoid, also referred to as a colonoid, was generated from an adenoma (associated with a resection surgery of an invasive moderately differentiated colorectal adenocarcinoma) as part of the development of an on-going organoid biobank at the Michigan Medicine Translational Tissue Modeling Laboratory (TTML, www.UmichTTML.org). The genomic variant signature of this adenoma colonoid was characterized using whole exome sequencing in order to access genomic concordance between the source patient tissue (adenoma and histologically normal tissue 10 cm from lesion) and the in vitro culture, as well as to access genomic stability of the culture over time at 2 and 6.5 months in culture.

2020-12-22 | E-MTAB-9936 | biostudies-arrayexpress

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