Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human Plexiform Leiomyomata provide further evidence for genetic heterogeneity underlying uterine fibroids

ABSTRACT: Plexiform leiomyomata are a histologically defined subgroup of benign uterine smooth muscle tumors based on their epitheliod cytology and abundant extracellular matrix. We used microarrays to compare plexiform leiomyomata to normal myometrium (smooth muscle of the uterine wall), typical leiomyomata, cellular or atypical leiomyomata and malignant leiomyosarcoma of the uterus. Experiment Overall Design: Samples analyzed on U133 Plus 2.0 and HuFL (GPL570 and GPL80). Experiment Overall Design: Data from the microarrays was merged by selection data for probe sets in which Entrez gene ID code on the GPL570 table equaled the Entrez gene ID on the GPL80 table. Experiment Overall Design: If more than one row on the GPL570 matched the value of the Entrez gene ID for a probe set on the GPL80 table, the values from the GPL570 were averaged. Thus, the GPL570 data was condensed to conform to the GPL80 format. Experiment Overall Design: The reformated raw data from both microarrays was then normalized such that the sum of the expression values was 3 million, and that values less than 20 were subsequently set to 20 (to permit log transformation in some statistical analysis).

ORGANISM(S): Homo sapiens

SUBMITTER: Bradley Quade

PROVIDER: E-GEOD-9511 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Molecular and cytogenetic characterization of plexiform leiomyomata provide further evidence for genetic heterogeneity underlying uterine fibroids.

Hodge Jennelle C JC Quade Bradley J BJ Rubin Mark A MA Stewart Elizabeth A EA Dal Cin Paola P Morton Cynthia C CC

The American journal of pathology 20080410 5

The plexiform variant of uterine leiomyomata (UL) is named for its ribbons or nests of smooth muscle cells that have a rounded, epithelioid shape caused by their entrapment in abundant extracellular matrix. Plexiform UL are currently classified as epithelioid smooth muscle tumors alongside the less predictable, "true" epithelioid tumors (ie, leiomyoblastomas). Karyotypes of six plexiform UL cases were studied, and their abnormalities were found to differ from those of leiomyoblastomas. Analyses ...[more]

PMID: 18403592

Similar Datasets

Project description:This series represent several subgroups of experiments designed to investigate the role of basal immunoglobulin signaling in immature B cell development. The first subgroup of arrays (Ctrl Mhi, Cre Mhi, Cre Mlo) was done to identify the changes in gene expression in immature B cells as a consequence of inducible deletion of surface IgM expression via Cre-LoxP mediated excision of Ig heavy chain. The second subgroup of arrays (GFPneg, GFPpos, FxE Ctrl, FxE HA) was done to identify the changes in gene expression in immature B cells as a consequence of blockade of tyrosine kinase signaling with herbimycin A treatment. The third subgroup of arrays (FxD, FxE, B6 Mneg, HEL Mhi) was done to establish gene expression profiles of immature B, pre B and pro B cells as reference platforms for the other two subgroups. (Tze etal. Public Library of Science Biology, 2005) The appended supplementary tables are described as follows: TABLE 1: Transformed array signal intensities used for statistical analysis. Listed are all probe sets excluding masked probe sets and Affymetrix hybridization control probe sets. Results are based on the following definitions: - Values with detection p values <0.1 were considered present. - Signal intensities with detection = "A" or with values < 20 were set to "20". TABLE 2: Genes differentially expressed between Ctrl Mhi and Cre Mlo cell populations and associated signal values. Results are based on the following definitions: - 2-fold or greater difference in means - difference in mean expression values > 200 - P < 0.01 (by Student's T test) TABLE 3: Probesets used for clustering in Figures 2 and 3 of publication TABLE 4: Probesets used for clustering in Figure 7 of publication TABLE 5: Correlation coefficients between all cell populations. Correlation coefficients were calculated as an additional method to demonstrate the relationship of the various cell populations to each other. Shown are the correlation coefficients generated using the mean expression values for each of the 101 transcripts from Figure 7 of publication. Keywords = bone marrow B cells

Project description:Increasing evidences have been recently reported on tumor cells heterogeneity within several malignancies, but data on liver tumours are still lacking. The aim of this study was to investigate and characterize tumor initiating cell (TIC) compartments within human hepatocellular carcinoma (HCC). After long term culture, we were able to identify 3 morphologically different tumor cell populations from an individual HCC specimen. These cell populations were extensively characterized by flow cytometry, fluorescence microscopy, single cell cloning, xenotransplantation in NOD/SCID IL2Rgamma -/- mice, karyotyping and microarray analyses. The 3 primary cell populations, hcc-1, -2 and -3, and the 2 clones (clone-1/7 and -1/8) generated by limiting dilution from hcc-1 showed different expression profiles for several tumor associated stem cell markers, including EpCAM, CD49f, CD44, CD133, CD56, Thy-1, ALDH and CK19. Moreover, they showed different doubling time and drug resistance. The tumorigenic potential was higher for hcc-1 and clone-1/7. Karyotyping analyses revealed a clonal evolution of cell populations and clones within the primary tumor. Importantly, we noticed that the primary tumor cell population with a higher tumorigenic potential and drug resistance was that showing more chromosomal alterations and containing different clones with both epithelial and mesenchymal features. Individual HCC can harbor different self-renewing tumorigenic cell types expressing a variety of morphology and phenotypic markers, karyotypic evolution and different gene expression profiles. This finding suggests that the therapeutic approach for HCC eradication should take into account the possible TIC heterogeneity due to intratumor clonal evolution. The aim was to analyse the whole genome expression profile of 3 HCC cell lines (Hcc-1, Hcc-2 and Hcc-3) and two clones (Clone-1/7 and Clone-1/8) cells obtained from one patient. Tumor sample was dissociated and cells cultured on collagen coated Petri dishes. When cell colonies appeared in culture, they were detached and cultured separately; clones were obtained fron HCC-1 cell lines by means of limiting dilution. Total Five independent total RNA extractions were performed for each cell line and clone and after checked the quality, concentration and integrity of the purified RNA, only samples showing the better results were chosen to be further processed. After the acquisition of the raw intensity data matrix with the corresponding annotations, probes corresponding to "predicted" genes or not associated to a Entrez ID were discarded from the analysis; moreover, different probe signals corresponding to the same Entrez ID were converted into unique intensity signal, corresponding to the median of the values for each array, in order to obtain a single signal for each Entrez ID. After this process, we generated a boxplot of 16964 intensity signals whose values were log2-transformed and quantile normalized using the aroma.light package for Bioconductor. Genes with a differential expression value of at least 2 fold (on log2 transformed scale) were considered differentially expressed.

Dataset Information

Transcription profiling of human Plexiform Leiomyomata provide further evidence for genetic heterogeneity underlying uterine fibroids

Publications

Molecular and cytogenetic characterization of plexiform leiomyomata provide further evidence for genetic heterogeneity underlying uterine fibroids.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets