Tissue Bank
Bioinformatics

BIOINFORMATICS PORTAL



A set of published breast cancer papers containing experimental data from differential expression, proteomics and copy number variations has been manually curated, with the results loaded into a relational database.

The data was annotated and integrated with available Ensembl human genome annotations, including gene related annotations, sequences, SNPs and pathway information from KEGG and Reactome. We update the database on a regular basis and welcome content suggestions from scientists.



Portal Statistics

ITEMCOUNT
No. of Curated Papers
72
No. of Datasets
135

TRANSCRIPTOMICS
Author(s)TitleJournalDate
Andre F et al

Exonic expression profiling of breast cancer and benign lesions: a retrospective analysis

Lancet Oncol

2009

Bild A et al

Oncogenic pathway signatures in human cancers as a guide to targeted therapies

Nature

2006

Boersma BJ

A stromal gene signature associated with inflammatory breast cancer

Int J Cancer

2008

Bos P et al

Genes that mediate breast cancer metastasis to the brain

Nature

2009

Burga L et al

Altered proliferation and differentiation properties of primary mammary epithelial cells from BRCA1 mutation carriers

Cancer Res

2009

Casey T et al

Molecular signatures suggest a major role for stromal cells in development of invasive breast cancer

Breast Cancer Res Treat

2009

Chang J et al

Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer

Lancet

2003

Charafer-Jauffret et al

Breast Cancer Cell Lines Contain Functional Cancer Stem Cells with Metastatic Capacity and a Distinct Molecular Signature

Cancer Res

2009

Chen D et al

Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue

Breast Cancer Res Treat

2010

Creighton C et al

Development of resistance to targeted therapies transforms the clinically associated molecular profile subtype of breast tumor xenografts

Cancer Res

2008

Desmedt C et al

Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series

Clin Cancer Res

2007

Emery L et al

Early dysregulation of cell adhesion and extracellular matrix pathways in breast cancer progression

Am J Pathol

2009

Farmer P et al

Identification of molecular apocrine breast tumours by microarray analysis

Oncogene

2005

Farmer P et al

A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer

Nat Med

2009

Finak G et al

Stromal gene expression predicts clinical outcome in breast cancer

Nat Med

2008

Furuta S et al

Removal of BRCA1/CtIP/ZBRK1 repressor complex on ANG1 promoter leads to accelerated mammary tumor growth contributed by prominent vasculature

Cancer cell

2006

Ginestier C et al

Prognosis and gene expression profiling of 20q13-amplified breast cancers

Clin Cancer Res

2006

Graham K et al

Gene expression in histologically normal epithelium from breast cancer patients and from cancer-free prophylactic mastectomy patients shares a similar profile

Br J Cancer

2010

Hennessy B et al

Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics

Cancer Res

2009

Hess K et al

Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer

J Clin Oncol

2006

Hu Z et al

The molecular portraits of breast tumors are conserved across microarray platforms

BMC Genomics

2006

Huang E et al

Gene expression predictors of breast cancer outcomes

Lancet

2003

Huang F et al

Identification of candidate molecular markers predicting sensitivity in solid tumors to dasatinib: rationale for patient selection

Cancer Res

2007

Ivshina A et al

Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer

Cancer Res

2006

Korkola J et al

Differentiation of lobular versus ductal breast carcinomas by expression microarray analysis

Cancer Res

2003

Kote-Jarai Z et al

Accurate prediction of BRCA1 and BRCA2 heterozygous genotype using expression profiling after induced DNA damage

Clin Cancer Res

2006

Kreike B et al

Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas

Breast Cancer Res

2007

Latimer J et al

Nucleotide excision repair deficiency is intrinsic in sporadic stage I breast cancer

Proc Natl Acad Aci USA

2010

Lee S et al

Alterations of gene expression in the development of early hyperplastic precursors of breast cancer

Am J Pathology

2007

Lee S et al

Differentially expressed genes regulating the progression of ductal carcinoma in situ to invasive breast cancer

Cancer Res

2012

Lerebours F et al

miRNA expression profiling of inflammatory breast cancer identifies a 5-miRNA signature predictive of breast tumor aggressiveness

Int J Cancer

2013

Lim E et al

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

Nat Med

2009

Ma X et al

Gene expression profiling of the tumor microenvironment during breast cancer progression

Breast Cancer Res

2009

Ma X et al

A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen

Cancer Cell

2004

Miller L et al

An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival

PNAS

2005

Miller WR et al

Changes in breast cancer transcriptional profiles after treatment with the aromatase inhibitor, letrozole

Pharmacogenet Genomics

2007

Minn AJ et al

Genes that mediate breast cancer metastasis to lung

Nature

2005

Mittempergher L et al

A gene signature for late distant metastasis in breast cancer identifies a potential mechanism of late recurrences

Mol Oncol

2013

Naderi A et al

A gene-expression signature to predict survival in breast cancer across independent data sets

Oncogene

2007

Nagaraja G et al

Gene expression signatures and biomarkers of noninvasive and invasive breast cancer cells: comprehensive profiles by representational difference analysis, microarrays and proteomics

Oncogene

2006

Neve R et al

A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes

Cancer Cell

2006

Paik S et al

A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer

N Engl J Med

2004

Parker J et al

Supervised risk predictor of breast cancer based on intrinsic subtypes

J Clin Oncol

2009

Pawitan Y et al

Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts

Breast Cancer Res

2005

Persson H et al

Identification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene

Cancer Res

2011

Poola I et al

Identification of MMP-1 as a putative breast cancer predictive marker by global gene expression analysis

Nat Med

2005

Riggins R et al

ERRgamma mediates tamoxifen resistance in novel models of invasive lobular breast cancer

Cancer Res

2008

Ring B et al

Novel prognostic immunohistochemical biomarker panel for estrogen receptor positive breast cancer

J Clin Oncol

2006

Saal L et al

Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity

PNAS

2007

Schuetz C et al

Progression-specific genes identified by expression profiling of matched ductal carcinomas in situ and invasive breast tumors, combining laser capture microdissection and oligonucleotide microarray analysis

Cancer Res

2006

Sorlie T et al

Repeated observation of breast tumor subtypes in independent gene expression data sets

PNAS

2003

Sotiriou C et al

Breast cancer classification and prognosis based on gene expression profiles from a population-based study

PNAS

2003

Sotiriou C et al

Gene Expression Profiling in Breast Cancer: Understanding the molecular basis of histologic grade to improve prognosis

J Natl Cancer Inst

2006

Turashvili G et al

Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis

BMC Cancer

2007

van't Veer LJ et al

Gene expression profiling predicts clinical outcome of breast cancer

Nature

2002

Zhao H et al

Different gene expression patterns in invasive lobular and ductal carcinomas of the breast

Mol Biol Cell

2004

Wang Y et al

Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer

Lancet

2005

miRNA
Authors(s)TitleJournalDate
Iorio et al

MicroRNA gene expression deregulation in human breast cancer

Cancer Res

2005

Maillot G et al

Widespread estrogen-dependent repression of micrornas involved in breast tumor cell growth

Cancer Res

2009

Van der Auwera I et al

Integrated miRNA and mRNA expression profiling of the inflammatory breast cancer subtype

Br J Cancer

2010

Volinia et al

A microRNA expression signature of human solid tumors defines cancer gene targets

PNAS

2006

Wu Q et al

Next-generation sequencing of microRNAs for breast cancer detection

J Biomed Biotechnol

2011

METHYLOMICS
Author(s)TitleJournalDate
Bediaga N et al

DNA methylation epigenotypes in breast cancer molecular subtypes

Breast Cancer Res

2010

Dedeurwaerder S et al

DNA methylation profiling reveals a predominant immune component in breast cancers

EMBO Mol Med

2011

Heyn H et al

DNA methylation profiling in breast cancer discordant identical twins identifies DOK7 as novel epigenetic biomarker

Carcinogenesis

2013

Holm K et al

Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns

Breast Cancer Res

2010

Li L et al

Estrogen and progesterone receptor status affect genome-wide DNA methylation profile in breast cancer

Hum Mol Genet

2010

PROTEOMICS
Author(s)TitleJournalDate
Gromov P et al

Up-regulated proteins in the fluid bathing the tumour cell microenvironment as potential serological markers for early detection of cancer of the breast

Mol Oncol

2010

Kulasingam V et al

Proteomics analysis of conditioned media from three breast cancer cell lines

Mol Cell Proteomics

2007

Moreira JMA et al

Tissue proteomics of the human mammary gland: Towards an abridged definition of the molecular phenotypes underlying epithelial normalcy

Mol Oncol

2010

Xu X et al

Quantitative proteomics study of breast cancer cell lines isolated from a single patient: Discovery of TIMM17A as a marker for breast cancer

Proteomics

2010

Zhang D et al

Proteomic study reveals that proteins involved in metabolic and detoxification pathways are highly expressed in HER-2/neu-positive breast cancer

Mol Cell Proteomics

2005