PROBE-LEVEL UNIVERSAL SEARCH (PLUS) ALGORITHM FOR GENDER DIFFERENTIATION IN AFFYMETRIX DATASETS

2010 ◽  
Vol 08 (03) ◽  
pp. 553-577 ◽  
Author(s):  
ANNA S. KARYAGYNA ◽  
MICHAIL O. VASSILIEV ◽  
ANNA S. ERSHOVA ◽  
RAMIL N. NURTDINOV ◽  
ILYA S. LOSSEV
Keyword(s):  
Gene Expression ◽  
Sex Chromosome ◽  
Perfect Match ◽  
Selection Procedure ◽  
Single Measure ◽  
Gender Differentiation ◽  
Affymetrix Microarrays ◽  
Individual Good ◽  
New Feature ◽  
Probe Set

Affymetrix microarrays measure gene expression based on the intensity of hybridization of a panel of oligonucleotide probes (probe set) with mRNA. The signals from all probes within a probe set are converted into a single measure that represents the expression value of a gene. This step diminishes the number of independently measured parameters and eliminates from consideration individual "good-working" probes. We propose a new feature selection algorithm (Probe Level Universal Search or PLUS algorithm) for probe-level analysis of gene expression datasets. The algorithm evaluates the intensities of perfect-match Affymetrix probes individually and selects probes that allow one to distinguish two given classes of samples. The algorithm was used to differentiate the samples according to their gender ("gender differentiation"). The universal gender differentiating set of 3' Gene Affymetrix microarray probes was selected; the set consists of 38 probes from XIST gene of X-chromosome and 17 probes from five Y-chromosome genes: RPS4Y1, EIF1A, DDX3Y, JARID1D and USP9Y. The selection procedure based on the probes selected by PLUS algorithm differentiates the sex chromosome karyotype of the sample, reveals samples with incorrect gender labels and samples from patients with hereditary syndromes or cancer-associated chromosome abnormalities.

scholarly journals Microarray Analyses of Gene Expression during Chondrocyte Differentiation Identifies Novel Regulators of Hypertrophy

2005 ◽  
Vol 16 (11) ◽  
pp. 5316-5333 ◽  
Author(s):  
Claudine G. James ◽  
C. Thomas G. Appleton ◽  
Veronica Ulici ◽  
T. Michael Underhill ◽  
Frank Beier
Keyword(s):  
Gene Expression ◽  
Bone Development ◽  
Skeletal Development ◽  
Expression Patterns ◽  
Chondrocyte Differentiation ◽  
Endochondral Bone ◽  
Temporal Gene Expression ◽  
Affymetrix Microarrays ◽  
Time Period ◽  
And Cluster Analysis

Ordered chondrocyte differentiation and maturation is required for normal skeletal development, but the intracellular pathways regulating this process remain largely unclear. We used Affymetrix microarrays to examine temporal gene expression patterns during chondrogenic differentiation in a mouse micromass culture system. Robust normalization of the data identified 3300 differentially expressed probe sets, which corresponds to 1772, 481, and 249 probe sets exhibiting minimum 2-, 5-, and 10-fold changes over the time period, respectively. GeneOntology annotations for molecular function show changes in the expression of molecules involved in transcriptional regulation and signal transduction among others. The expression of identified markers was confirmed by RT-PCR, and cluster analysis revealed groups of coexpressed transcripts. One gene that was up-regulated at later stages of chondrocyte differentiation was Rgs2. Overexpression of Rgs2 in the chondrogenic cell line ATDC5 resulted in accelerated hypertrophic differentiation, thus providing functional validation of microarray data. Collectively, these analyses provide novel information on the temporal expression of molecules regulating endochondral bone development.

scholarly journals Cardiac myocyte gene expression profiling during H2O2-induced apoptosis

2007 ◽  
Vol 29 (2) ◽  
pp. 118-127 ◽  
Author(s):  
Angela Clerk ◽  
Timothy J. Kemp ◽  
Georgia Zoumpoulidou ◽  
Peter H. Sugden
Keyword(s):  
Gene Expression ◽  
Cardiac Myocytes ◽  
Cardiac Myocyte ◽  
Apoptotic Response ◽  
Dynamic Changes ◽  
Affymetrix Microarrays ◽  
Low Concentrations ◽  
Alternatively Spliced ◽  
Induced Apoptosis ◽  
Cardiac Myocyte Apoptosis

High levels of oxidative stress promote cardiac myocyte death, though lower levels are potentially cytoprotective/anabolic. We examined the changes in gene expression in rat neonatal cardiac myocytes exposed to apoptotic (0.2 mM) or nontoxic (0.04 mM) concentrations of H2O2 (2, 4, or 24 h) using Affymetrix microarrays. Using U34B arrays, we identified a ubiquitously expressed, novel H2O2-responsive gene [putative peroxide-inducible transcript 1 (Perit1)], which generates two alternatively spliced transcripts. Using 230 2.0 arrays, H2O2 (0.04 mM) promoted significant changes in expression of only 32 genes, all of which were seen with 0.2 mM H2O2. We failed to detect any increase in the rate of protein synthesis in cardiac myocytes exposed to <0.1 mM H2O2, further suggesting that global, low concentrations of H2O2 are not anabolic in this system. H2O2 (0.2 mM) promoted significant ( P < 0.05, >1.75-fold) changes in expression of 649 mRNAs and 187 RNAs corresponding to no established gene. Of the mRNAs, 114 encoded transcriptional regulators including Krüppel-like factors (Klfs). Quantitative PCR independently verified the changes in Klf expression. Thus, H2O2-induced cardiac myocyte apoptosis is associated with dynamic changes in gene expression. The expression of these genes and their protein products potentially influences the progression of the apoptotic response.

ENTROPY-BASED CLUSTER VALIDATION AND ESTIMATION OF THE NUMBER OF CLUSTERS IN GENE EXPRESSION DATA

2012 ◽  
Vol 10 (05) ◽  
pp. 1250011
Author(s):  
NATALIA NOVOSELOVA ◽  
IGOR TOM
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Clustering Algorithm ◽  
Selection Procedure ◽  
Biological Knowledge ◽  
Consensus Clustering ◽  
Expression Data ◽  
Cluster Validation ◽  
Number Of Clusters ◽  
Validity Measure

Many external and internal validity measures have been proposed in order to estimate the number of clusters in gene expression data but as a rule they do not consider the analysis of the stability of the groupings produced by a clustering algorithm. Based on the approach assessing the predictive power or stability of a partitioning, we propose the new measure of cluster validation and the selection procedure to determine the suitable number of clusters. The validity measure is based on the estimation of the "clearness" of the consensus matrix, which is the result of a resampling clustering scheme or consensus clustering. According to the proposed selection procedure the stable clustering result is determined with the reference to the validity measure for the null hypothesis encoding for the absence of clusters. The final number of clusters is selected by analyzing the distance between the validity plots for initial and permutated data sets. We applied the selection procedure to estimate the clustering results on several datasets. As a result the proposed procedure produced an accurate and robust estimate of the number of clusters, which are in agreement with the biological knowledge and gold standards of cluster quality.

scholarly journals BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2748 ◽  
Author(s):  
Andrea Komljenovic ◽  
Julien Roux ◽  
Marc Robinson-Rechavi ◽  
Frederic B. Bastian
Keyword(s):  
Gene Expression ◽  
Gene List ◽  
R Package ◽  
Rna Seq ◽  
Anatomical Structures ◽  
Enrichment Test ◽  
Expression Of Genes ◽  
Affymetrix Microarrays ◽  
New Gene

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and reprocessed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages. Moreover, BgeeDB includes a new gene set enrichment test for preferred localization of expression of genes in anatomical structures (“TopAnat”). Along with the classical Gene Ontology enrichment test, this test provides a complementary way to interpret gene lists. Availability: http://www.bioconductor.org/packages/BgeeDB/

scholarly journals Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline

PLoS Biology ◽  
2016 ◽  
Vol 14 (7) ◽  
pp. e1002499 ◽  
Author(s):  
Emily L. Landeen ◽  
Christina A. Muirhead ◽  
Lori Wright ◽  
Colin D. Meiklejohn ◽  
Daven C. Presgraves
Keyword(s):  
Gene Expression ◽  
Sex Chromosome ◽  
Regulatory Evolution ◽  
Male Germline ◽  
Transcriptional Suppression

Gene Expression Profiling of Isolated Mesenchymal and Osteoblastic Cells Exhibits a Different Pattern of Expression in Multiple Myeloma Patients as Compared to Healthy Subjects: Potential Relationship with the Presence of Bone Lesions.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3513-3513
Author(s):  
Nicola Giuliani ◽  
Katia Todoerti ◽  
Gina Lisignoli ◽  
Sara Tagliaferri ◽  
Luca Agnelli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Cell Proliferation ◽  
Osteogenic Differentiation ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Differentially Expressed ◽  
Bone Lesions ◽  
Bone Status ◽  
Probe Set

Abstract Gene expression alterations occurring in the bone microenvironment cells and their potential relationships with the occurrence of bone lesions in multiple myeloma (MM) patients have never been investigated. In this study, we have isolated both mesenchymal (MSC) and osteoblastic (OB) cells, without in vitro differentiation, from bone biopsies obtained by iliac crest of 24 MM patients, 7 MGUS subjects and 8 healthy donors (N) who underwent orthopedics surgery. Bone status was evaluated in all MM patients by total X rays scan and MRI for the spine. Firstly, we evaluated cell proliferation in relationship with growth substrate (bone and glass) and cell phenotype by flow cytometry and immunohistochemistry. We found that both MSC and OB cells have higher cell doubling rate in MM patients as compared to N. Higher expression of alkaline phosphatase and Runx2 was observed in OB as compared to MSC cells in both N and MM patients without osteolytic lesions, but not in osteolytic ones. We performed a gene expression profiling analysis of isolated MSC and OB cells using GeneChip® Affymetrix HG-U133A oligonucleotide arrays. An unsupervised analysis of the most variable genes across the dataset generated a hierarchical clustering with the two major branches containing respectively MSC and OB samples. A multiclass analysis of N, MGUS and MM patients identified 33 differentially expressed probe-set (specific for 27 genes) in MSC cells, and 19 differentially expressed probe-set (13 genes) in OB, and the identified transcripts mainly characterized N versus MM and MGUS samples. A supervised analysis between N and MM samples identified 65 probes (56 genes: 17 up-regulated and 39 down-regulated) differentially expressed in MSC and 35 probes (29 genes, 12 up-regulated and 17 down-regulated) in OB. Notably, genes encoding the Homeobox class proteins, such as HOXB2-6-7, were up-regulated in both MSC and OB of MM patients as compared to N. As regards the bone status, a total of 60 probe-sets (3 up-regulated and 57 down-regulated genes) were found differentially expressed in MSC from osteolytic vs. non-osteolytic MM patients, whereas MGUS-MSC exhibited an intermediate transcriptional profile between osteolytic and non-osteolytic MM patients. A distinct pattern of gene expression profiling was also observed in MSC versus OB when osteolytic and non-osteolytic MM patients were compared (26 vs. 94 differentially expressed probe-sets, respectively), including transcription factors related to MSC osteogenic differentiation belonging to Runx2 pathway (HEY1) or Wnt and BMP signaling On the other hand, few genes were found differentially expressed in OB cells in relationship with the presence of bone lesions. In conclusion, we identified a distinctive transcriptional fingerprint in isolated MSC and OB cells of MM patients as compared to N subjects, which mainly correlated with cell proliferation. Moreover, a different gene expression profile was observed in MSC cells of MM patients according to the presence/absence of bone lesions, highlighting the critical role of the block of the osteogenic differentiation.

scholarly journals Finding a Balance: How Diverse Dosage Compensation Strategies Modify Histone H4 to Regulate Transcription

2012 ◽  
Vol 2012 ◽  
pp. 1-12
Author(s):  
Michael B. Wells ◽  
Györgyi Csankovszki ◽  
Laura M. Custer
Keyword(s):  
Gene Expression ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Current Understanding ◽  
Histone H4 ◽  
Linked Gene ◽  
Expression Levels ◽  
Gene Expression Levels

Dosage compensation balances gene expression levels between the sex chromosomes and autosomes and sex-chromosome-linked gene expression levels between the sexes. Different dosage compensation strategies evolved in different lineages, but all involve changes in chromatin. This paper discusses our current understanding of how modifications of the histone H4 tail, particularly changes in levels of H4 lysine 16 acetylation and H4 lysine 20 methylation, can be used in different contexts to either modulate gene expression levels twofold or to completely inhibit transcription.

Sign in / Sign up

Export Citation Format

Share Document