Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of Novel Cholesteatoma-related Gene Expression Signatures Using Full-genome Microarrays

ABSTRACT: In this study, we investigated differentially expressed genes in human cholesteatomas in comparison to regular auditory canal skin using Whole Human Genome Microarrays that contain 19,596 human genes. In addition to already described up-regulated mRNAs in cholesteatoma, such as MMP9, DEFB2 and KRT19, we identified 3558 new cholesteatoma-related transcripts. 811 genes appear to be significantly differentially up-regulated in cholesteatoma. 334 genes were down-regulated more than 2-fold. Significantly regulated genes with protein metabolism activity include matrix metalloproteinases as well as PI3, SERPINB3 and SERPINB4. Genes like SPP1, KRT6B, PRPH, SPRR1B and LAMC2 are known as genes with cell growth and/or maintenance activity. Transport activity genes and signal transduction genes are LCN2, GJB2 and CEACAM6. The three cell communication genes are CDH19 and genes belonging to the S100 family.

ORGANISM(S): Homo sapiens

PROVIDER: GSE42256 | GEO | 2012/11/14

SECONDARY ACCESSION(S): PRJNA179448

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of Novel Cholesteatoma-related Gene Expression Signatures Using Full-genome Microarrays

Project description:In this study, we investigated differentially expressed genes in human cholesteatomas in comparison to regular auditory canal skin using Whole Human Genome Microarrays that contain 19,596 human genes. In addition to already described up-regulated mRNAs in cholesteatoma, such as MMP9, DEFB2 and KRT19, we identified 3558 new cholesteatoma-related transcripts. 811 genes appear to be significantly differentially up-regulated in cholesteatoma. 334 genes were down-regulated more than 2-fold. Significantly regulated genes with protein metabolism activity include matrix metalloproteinases as well as PI3, SERPINB3 and SERPINB4. Genes like SPP1, KRT6B, PRPH, SPRR1B and LAMC2 are known as genes with cell growth and/or maintenance activity. Transport activity genes and signal transduction genes are LCN2, GJB2 and CEACAM6. The three cell communication genes are CDH19 and genes belonging to the S100 family. Two samples from each patient (cholesteatoma vs. normal auditory canal skin) for each two-colour hybridisation experiment

2012-11-14 | E-GEOD-42256 | biostudies-arrayexpress

Fibroblasts in cholesteatoma activate osteoclasts.

Project description:Cholesteatoma arises from a tympanic membrane and expands in the middle ear. It erodes the surrounding bone and leads to hearing loss or brain abscess which is lethal complication. Currently, the only effective treatment is the complete surgical removal of cholesteatoma. However, possibility of recurrence is not satisfactory, other clinical treatment is desired. A mechanism of bone erosion in rheumatoid arthritis, which is one of the bone destructive disease, is progressing to be clarified. Receptor activator of NF-κB ligand (RANKL) secreted by synovial fibroblasts, T cells, and B cells lead to differentiation and activation of osteoclast precursor in rheumatoid arthritis. In contrast it has been still unclear why cholesteatoma erodes bone. In the current study we studied that osteoclasts statistically increased in cholesteatoma, and that fibroblasts in the prematrix of cholesteatoma express RANKL. In this study we studied that osteoclasts statistically increased in cholesteatoma, and that fibroblasts in the prematrix of cholesteatoma express RANKL. We investigated upstream of RANKL from RNA sequence results by Ingenuity Pathways Analysis, which is data base of abundance information about molecular biology.

2019-06-30 | GSE116142 | GEO

Circular RNAs show differential expression profiles and may be potential therapeutic targets by acting as ceRNAs in cholesteatoma

Project description:In our present study, we explored the circRNA expression profiles in cholesteatoma by deep RNA-seq analysis. We obtained totally 355 significantly differentially expressed circRNA in cholesteatoma, among which 101 were identified to be up-regulated, and 254 down-regulated. By constructing the circRNA-miRNA-mRNA ceRNA networks, it was discovered that circRNAs might contribute to cholesteatoma formation by functioning as ceRNAs for miRNAs.

2020-04-27 | GSE102715 | GEO

Large scale proteomics of cholesteatoma

Project description:The study describes comprehensive proteomics data of the cholesteatoma disease. Cholesteatoma is a serious and destructive growth of keratinizing squamous epithelium in the middle ear, with a poorly understood etiopathogenesis. The large scale proteomics approach used in this study highly expands our molecular knowledge of cholesteatoma and implicates several biological functions in its pathology. Human samples of cholesteatoma, neck of cholesteatoma, tympanic membrane, external auditory canal skin, and middle ear mucosa were analyzed. Approximately two thousand unique proteins were identified by label-free nanoLC-MS/MS proteomics. The protein and peptide identification data were obtained by Proteome Discoverer (Thermo Scientific, version 1.3.0.339) processing of LTQ Orbitrap raw files using the Mascot algorithm (Matrix Sciences, version 2.4.0). To yield comprehensive proteome data the tissue biopsy was separated into ten protein fractions, which were MS analysed separately, and the resulting MS files were subsequently merged in the database analysis. Precursor mass tolerance was 5 ppm and fragment mass tolerance was 0.5 Da. Dynamic Modification was Oxidation (M) and Static Modification was Carbamidomethyl (C); annotated in the PRIDE files as mass deviations (e g for double charged peptides m/z deviation of approximately 8.00 and 28.51 for modification of Met and Cys, respectively). FASTA file was SwissProt_2012_03.fasta (containing 20,255 Homo sapiens sequences). MudPit scoring was applied, and up to two missed trypsin cleavages were accepted. Peptide cut off Score was 10 and protein relevance threshold was 20.

2014-06-04 | PXD000457 | Pride

Single-cell transcriptomics of human cholesteatoma identifies an activin A-producing osteoclastogenic fibroblast subset inducing bone destruction

Project description:To elucidate the mechanism underlying bone erosion in cholesteatoma, we performed scRNA-seq using human cholesteatoma tissues surgically resected from patients. We focused on pathogenic fibroblasts or keratinocytes, and therefore CD45-negative cells were collected for scRNA-seq analysis to exclude hematopoietic cell lineages. As there are no “normal” tissues in the middle ear that correspond to cholesteatoma, retroauricular skin at the incision site was used as the control for analysis of cholesteatoma. We dentified a characteristic pathogenic fibroblast subset with abundant expression of inhibin βA.

2023-05-29 | GSE210261 | GEO

Microarray analysis and functional prediction of differentially-expressed circular RNAs in acquired middle ear cholesteatoma

Project description:To investigate the differential expression profiling of circular RNAs (circRNAs) between acquired middle ear cholesteatoma and normal skin, and to identify potential circRNAs contributing to the etiopathogenesis of middle ear cholesteatoma, circRNA microarray analysis and functional prediction were performed.

2021-12-23 | GSE171006 | GEO

Fibroblasts in cholesteatoma activate osteoclasts.

Project description:Fibroblasts in cholesteatoma activate osteoclasts.

| PRJNA477370 | ENA

Genome-wide microarray analysis to identify the differentially expressed patterns of lncRNAs of cholesteatoma tissues compared with matched normal skin tissues.

Project description:We performed genome-wide microarray analysis to identify the differentially expressed patterns of lncRNAs in cholesteatoma. Our data indicated that lncRNA expression profiles were significantly altered in cholesteatoma compared with normal skin tissues. A total of 787 lncRNAs were identified (fold change ≥2.0, P < 0.05), consisting of 181 upregulated and 606 downregulated lncRNAs.

2018-05-09 | GSE102673 | GEO

Whole exome sequencing study of cholesteatoma patients from affected families

Project description:This study used whole exome sequencing on 21 patients with cholesteatoma from 10 families in order to identify variants that may attribute to cholesteatoma aetiology.

| EGAS00001006147 | EGA

TMT-based LC-MS/MS proteomics of cholesteatoma

Project description:Eight cases of middle ear cholesteatoma specimens and matched ear canal skin specimens

2023-03-07 | PXD036926 |