Breast Cancer Gene-Expression Miner v4.5
(bc-GenExMiner v4.5)
HOME
ANALYSIS
CORRELATION
Targeted
Exhaustive
Chromosomal location
EXPRESSION
Targeted
Exhaustive
Customised
PROGNOSTIC
Targeted
Exhaustive
Intrinsic molecular subtypes
Basal-like/TNBC
TUTORIAL
FLOWCHART
CORRELATION
Targeted
Exhaustive
Chromosomal location
EXPRESSION
Targeted
Exhaustive
Customised
PROGNOSTIC
Targeted
Exhaustive
Intrinsic molecular subtypes
Basal-like/TNBC
BACKGROUND
DATA CONTENT
Published annotated data
Published genomic data
Intrinsic molecular subtypes classification
DATA PRE-PROCESSING
DATA ANALYSIS
Statistical analyses
Statistical tests
Graphic illustrations
WHAT'S NEW?
HOW TO CITE US?
HOME
ANALYSIS
CORRELATION
Targeted
Exhaustive
Chromosomal location
EXPRESSION
Targeted
Exhaustive
Customised
PROGNOSTIC
Targeted
Exhaustive
Intrinsic molecular subtypes
Basal-like/TNBC
TUTORIAL
FLOWCHART
CORRELATION
Targeted
Exhaustive
Chromosomal location
EXPRESSION
Targeted
Exhaustive
Customised
PROGNOSTIC
Targeted
Exhaustive
Intrinsic molecular subtypes
Basal-like/TNBC
BACKGROUND
DATA CONTENT
Published annotated data
Published genomic data
Intrinsic molecular subtypes classification
DATA PRE-PROCESSING
DATA ANALYSIS
Statistical analyses
Statistical tests
Graphic illustrations
WHAT'S NEW?
HOW TO CITE US?
Targeted expression analysis
Enter input gene and choose one of the following options:
GENE EXPRESSION DATA
First, choose your gene expression data. Information about cohorts :
microarrays
,
Affymetrix
®,
METABRIC
,
TCGA
or SCAN-B (aka GSE81540 =
GSE81538
+
GSE96058
)
Then fill the textbox with actualised* gene symbol.
*: see actualised web databases (e.g.:
GeneCards
,
Ensembl
,
HGNC
,
NCBI Gene
...)
@: the probesets followed by "@" are described as references for subtyping ER, PR and HER2 status by means of genomics data. See
Kenn
et al.
.
DNA microarrays
All
(n = 10 001)
Affymetrix®
(n = 4 904)
METABRIC
(n = 1 980)
RNA-seq
All
(n = 4 712)
TCGA
(n = 1 034)
SCAN-B
(n = 3 678)
POPULATION
Choose one of the radio button to select which splitting method you want to explore for all patients.
Note: 51 years old is median age at menopause in western industrialised countries.
More details about molecular subtypes
here
.
Nature of the tissue (healthy, tumour-adjacent and tumour)
This analysis is only available with
TCGA data
.
This option allows you to split samples by the nature of the tissue.
There are 9 distinct analysis possibilities, each time comparing healthy (or normal) versus tumour-adjacent versus:
tumour tissue;
oestrogen receptor status;
progesterone receptor status;
oestrogen/progesterone receptor status combinations;
HER2 receptor status;
P53 status (sequence-based);
PAM50 breast cancer subtypes;
TNBC/non-TNBC;
basal-like (PAM50) & triple-negative breast cancer (IHC).
Receptor statuses (ER, PR and HER2 by IHC)
Nodal status
Histological types
SBR
NPI
Age
P53 status (IHC,
GES
and
sequence-based
)
Intrinsic molecular subtypes
This analysis split patients into groups bounded by multiple intrinsic molecular subtyping methods : "SSPs and RSSPC", "SCMs and RSCMC" and "RIMSPC".
More details
.
Basal-like (PAM50) and/or TNBC (IHC)
TNBC subtypes
This analysis is only available with
Affymetrix™ data
.
This option allows you to split triple-negative breast cancer (TNBC) samples and explore their three subtypes: C1, C2 and C3:
C1
: molecular apocrine tumours (or luminal androgen receptor);
C2
: basal-like tumours infiltrated by immune suppressive cells and high neurogenesis activity;
C3
: basal-like tumours triggering an ineffective immune response; which is associated with high tumour infiltrating lymphocytes and plasma cells; tertiary lymphoid structures and upregulation of immune checkpoints.
More details about TNBC subtypes classification
here
.
Integrative clusters (IntClust subtypes)
This analysis is only available with
METABRIC data
.
It permits to compare gene expression in the 10 integrative clusters (IntClust = iC)
Curtis et al., 2012
and
Dawson et al., 2013.
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Legend
ER:
oestrogen receptor
GES:
gene expression signature
HER2:
HER2 receptor
IHC:
immunohistochemistry
NPI:
Nottingham prognostic index
PAM50:
Parker's instrinsic molecular subtypes
PR:
progesterone receptor
SBR:
Scarff Bloom & Richardson grade
TNBC:
triple-negative breast cancer; tumours negative for oestrogen and progesterone receptors and growth factor receptor 2 (HER2), by means of IHC.
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2010
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Last update
June 22, 2020
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