GEO series

FoxA1 is a critical determinant of Estrogen Receptor function and endocrine response (part I)

GSE25314 Homo sapiens (human) Expression microarray 16 samples Submitted 2010/11/17 Platform GPL6947

At a glance

Expression microarray · human · 16 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 16 samples: 4 × vehicle vs 4 × estrogen vs 4 × estrogen and tamoxifen vs 4 × tamoxifenGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Estrogen Receptor-a (ER) is the key feature in the majority of breast cancers and ER binding to the genome correlates with the Forkhead protein FOXA1 (HNF3a), but mechanistic insight is lacking. We now show that FOXA1 is the defining factor that governs differential ER-chromatin interactions. We show that almost all ER-chromatin interactions and gene expression changes are dependent on the presence of FOXA1 and that FOXA1 dictates genome-wide chromatin accessibility.

Read the full summary ↓

Furthermore, we show that CTCF is an upstream negative regulator of FOXA1-chromatin interactions. In ER responsive breast cancer cells, the dependency on FOXA1 for tamoxifen-ER activity is absolute and in tamoxifen resistant cells, ER binding occurs independently of ligand, but in a FOXA1 dependent manner. Importantly, expression of FOXA1 in non-breast cancer cells is sufficient to alter ER binding and response to endocrine treatment. As such, FOXA1 is the primary determinant that regulates estrogen-ER activity and endocrine response in breast cancer cells and is sufficient to program ER functionality in non-breast cancer contexts.

This dataset

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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 (GSE25314_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 PRJNA142545. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21151129) ↗

Study design

4 × vehicle vs 4 × estrogen vs 4 × estrogen and tamoxifen vs 4 × tamoxifen

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM622757 vehicle replicate 1 vehicle
GSM622758 estrogen replicate 1 estrogen
GSM622759 estrogen and tamoxifen replicate 1 estrogen and tamoxifen
GSM622760 tamoxifen replicate 1 tamoxifen
GSM622761 vehicle replicate 2 vehicle
GSM622762 estrogen replicate 2 estrogen
GSM622763 estrogen and tamoxifen replicate 2 estrogen and tamoxifen
GSM622764 tamoxifen replicate 2 tamoxifen
GSM622765 vehicle replicate 3 vehicle
GSM622766 estrogen replicate 3 estrogen
GSM622767 estrogen and tamoxifen replicate 3 estrogen and tamoxifen
GSM622768 tamoxifen replicate 3 tamoxifen
GSM622769 vehicle replicate 4 vehicle
GSM622770 estrogen replicate 4 estrogen
GSM622771 estrogen and tamoxifen replicate 4 estrogen and tamoxifen
GSM622772 tamoxifen replicate 4 tamoxifen

Datasets on a similar topic

GSE245969 EP300/CREBBP acetyltransferase inhibition limits steroid receptor and FOXA1 signaling in prostate cancer cells 122 samples shares foxa1, receptor
GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares foxa1, receptor
GSE296419 The critical role of the host endogenous immune compartment after intracerebroventricular CAR T cell therapy in recurrent GBM 143 samples shares critical, part
GSE231290 Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle [RNAseq] 51 samples shares determinant, part
GSE280618 H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment 34 samples shares endocrine, estrogen
GSE244387 The retinoid X receptor has a critical role in synthetic rexinoid-induced increase in cellular all-trans-retinoic acid 24 samples shares critical, receptor
GSE280617 H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment [RNA-seq] 18 samples shares endocrine, estrogen
GSE280616 H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment [CUT&Tag] 16 samples shares endocrine, estrogen

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