Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human T-cell acute lymphoblastic leukemia, T-cell lymphoblastic lymphoma and B-precursor acute lymphoblastic leukemia samples

ABSTRACT: T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LL) and are often thought to represent a spectrum of a single disease. The malignant cells in T-ALL and T-LL are morphologically indistinguishable, and they share the expression of common cell surface antigens and cytogenetic characteristics. However, despite these similarities, differences in the predominant sites of disease in T-ALL and T-LL are observed. To determine if underlying biological distinctions may potentially contribute to some of these differences, we analyzed the global gene expression profiles of malignant T-cell precursors in ten T-ALL and nine T-LL using DNA arrays. Ten additional B-precursor ALL bone marrow samples, were used in a separate analysis.

Note that files GSM27087.txt and GSM27088.txt are identical as downloaded from GEO.

ORGANISM(S): Homo sapiens

DISEASE(S): B-precursor acute lymphoblastic leukemia

SUBMITTER: Dong-Joon Min

PROVIDER: E-GEOD-1577 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene expression profiling reveals intrinsic differences between T-cell acute lymphoblastic leukemia and T-cell lymphoblastic lymphoma.

Raetz Elizabeth A EA Perkins Sherrie L SL Bhojwani Deepa D Smock Kristi K Philip Mary M Carroll William L WL Min Dong-Joon DJ

Pediatric blood & cancer 20060801 2

<h4>Background</h4>T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LL) and are often thought to represent a spectrum of a single disease. The malignant cells in T-ALL and T-LL are morphologically indistinguishable, and they share the expression of common cell surface antigens and cytogenetic characteristics. However, despite these similarities, differences in the clinical behavior of T-ALL and T-LL are observed.<h4>Procedure</h4>We analyzed the gene expression pr ...[more]

PMID: 16358311

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Project description:Samples from 20 children with B-cell precursor ALL, comprising ten with high hyperdiploidy and ten with the ETV6/RUNX1 fusion, were included in the study. Four Âµg of methylated and input fraction DNA were analyzed with a classic MeDIP assay and subsequent microarray hybridization using the NimbleGen CpG Island-Plus-Promoter Array (Roche NimbleGen, Madison, WI).<br><br>This array platform covers all 28,226 UCSC-annotated CpG islands and promoter regions for all RefSeq genes, including 385,000 probes of 50-75mer length per array, with an upstream and downstream promoter tiling of 800 bp and 200 bp, respectively. Signal intensity data were extracted from the scanned images. Each feature on the array has a corresponding log2 ratio, which is the ratio of the input signals for the methylated DNA and the input fraction DNA. The log2 ratio was scaled in order to center the ratio data around zero by subtracting the bi-weight mean for the log2 ratio values for all features on the array from each log2 ratio value. A modified ACME algorithm, where a fixed-length window (750 bp) is placed around each consecutive probe, and the one-sided Kolmogorov-Smirnov test were then applied on the scaled log2 ratio data to determine whether the probes were drawn from a significantly more positive distribution (peak) of intensity log2 ratios than the other probes in the array. The resulting score for each probe is the -log10 p-value from the windowed Kolmogorov-Smirnov test around that probe. Peak data were generated by searching for probes above a p-value minimum cut-off (-log10) of 2.<br><br>Peaks within 500 bp of each other were merged. Each annotated gene was subsequently searched for peaks appearing in a specified promoter region around the transcription start site. The region searched was design-specific, spanning from 5 kb upstream to 1 kb downstream of the transcription start site. Genes that had at least two probes with peaks above the p-value minimum cut-off were considered to have significant CpG island methylation scores for hypermethylation.

Dataset Information

Transcription profiling of human T-cell acute lymphoblastic leukemia, T-cell lymphoblastic lymphoma and B-precursor acute lymphoblastic leukemia samples

Publications

Gene expression profiling reveals intrinsic differences between T-cell acute lymphoblastic leukemia and T-cell lymphoblastic lymphoma.

Similar Datasets

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