GEO series

Gene expression study of anaplastic large cell lymphomas: cellular origin, pathogenesis and relation to Hodgkin lymphoma

GSE14879 Homo sapiens (human) Expression microarray 64 samples Submitted 2009/11/16 Platform GPL570

At a glance

Expression microarray · human · 64 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Hodgkin lymphomaThis series is part of our curated briefing on it.
Samples: 64 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Anaplastic large cell lymphoma (ALCL) is a main type of T cell lymphomas and comprises three distinct entities: systemic ALK+, systemic ALK- and cutaneous ALK- ALCL. Little is known about their pathogenesis and their cellular origin, and morphological and immunophenotypical overlap exists between ALK- ALCL and classical Hodgkin lymphoma (cHL).

Read the full summary ↓

We conducted gene expression profiling of microdissected lymphoma cells of ALK+ and ALK- systemic ALCL, cutaneous ALCL and cHL, and of eight subsets of normal T and NK cells. The analysis supports a derivation of ALCL from activated T cells, but the lymphoma cells acquired a gene expression pattern hampering an assignment to a CD4+, CD8+ or CD30+ T cell origin. Indeed, ALCL display a general down-modulation of T cell characteristic molecules. All ALCL types show significant expression of NFκB target genes and upregulation of genes involved in oncogenesis (e.g. EZH2). Surprisingly few genes are differentially expressed between systemic and cutaneous ALK- ALCL despite their different clinical behaviour, and between ALK- ALCL and cHL despite their different cellular origin. ALK+ ALCL are characterized by expression of genes regulated by pathways constitutively activated by ALK. This study provides multiple novel insights into the molecular biology and pathogenesis of ALCL.

This dataset

Open GSE14879 in finder → Find more human microarray datasets → Hodgkin lymphoma landscape →

Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE14879_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA111939. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 19657361) ↗

Samples in this study

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+ 64 more — browse all 64 samples with per-sample file links →

More Hodgkin lymphoma datasets

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GSE289903 Gene expression profiling of HIV and EBV-associated classic Hodgkin lymphomas from Malawi 19 samples same disease briefing · shares lymphomas, lymphoma, hodgkin
GSE17920 Expression data of diagnostic biopsy samples from Hodgkin lymphoma patients 130 samples same disease briefing · shares lymphoma, hodgkin
GSE305165 Redefining the Spectrum of EBV-Positive Diffuse Large B-Cell Lymphoma and EBV-Positive Classic Hodgkin Lymphoma 47 samples same disease briefing · shares lymphoma, hodgkin
GSE22208 Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma 48 samples same disease briefing · shares lymphoma, hodgkin
GSE301492 Transcriptome sequencing of Hodgkin lymphoma Hodgkin and Reed-Sternberg cells reveals escape from NK cell recognition and an unfolded protein response 41 samples same disease briefing · shares lymphoma, hodgkin
GSE288623 Transcriptional profiles of the Hodgkin lymphoma tumor-associated macrophage in vitro models 24 samples same disease briefing · shares lymphoma, hodgkin
GSE290026 scRNA and TCR-Seq of peripheral blood mononuclear cells (PBMC) from r/r classical Hodgkin Lymphoma patients under anti-PD1 therapy. 23 samples same disease briefing · shares lymphoma, hodgkin

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