Breast Cancer Gene-Expression Miner v4.9
(bc-GenExMiner v4.9)
HOME
ANALYSIS
CORRELATION
Targeted
Exhaustive
Chromosomal location
EXPRESSION
Targeted
Exhaustive
Customised
PROGNOSTIC
Targeted
Exhaustive
Intrinsic molecular subtypes
TNBC/Basal-like
TNBC subtypes
TUTORIAL
FLOWCHART
CORRELATION
Targeted
Exhaustive
Chromosomal location
EXPRESSION
Targeted
Exhaustive
Customised
PROGNOSTIC
Targeted
Exhaustive
Intrinsic molecular subtypes
TNBC/Basal-like
TNBC subtypes
BACKGROUND
DATA CONTENT
Published annotated data
Published transcriptomic 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
TNBC/Basal-like
TNBC subtypes
TUTORIAL
FLOWCHART
CORRELATION
Targeted
Exhaustive
Chromosomal location
EXPRESSION
Targeted
Exhaustive
Customised
PROGNOSTIC
Targeted
Exhaustive
Intrinsic molecular subtypes
TNBC/Basal-like
TNBC subtypes
BACKGROUND
DATA CONTENT
Published annotated data
Published transcriptomic data
Intrinsic molecular subtypes classification
DATA PRE-PROCESSING
DATA ANALYSIS
Statistical analyses
Statistical tests
Graphic illustrations
WHAT'S NEW?
HOW TO CITE US?
Gene correlation targeted analysis
Enter input genes and choose one of the following options:
GENES 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(s).
For more than two genes, identifiers must be separated by ";" (e.g.: UBE2C;LMNB1).
*: see actualised web databases (e.g.:
Ensembl
,
GeneCards
,
HGNC
,
NCBI Gene
...)
DNA microarrays
All
(n = 11 359)
Clear
RNA-seq
All
(n = 4 421)
Upload a gene list file
(min. 2 to max. 20 genes)
The uploaded file must comply with all following criteria:
file with tabulation, space, comma or newline separated values,
file type from among the following extensions: .csv, .tsv or .txt,
file containing only gene symbols (not full names or descriptions),
file with a maximum items of 20 gene symbols,
file with a maximum size of 10 Kbytes.
POPULATION
Choose one of the radio button to select which population you want to explore.
All patients
Oestrogen receptor status
Progesterone receptor status
Oestrogen and progesterone receptors status combinations
Nodal status
Intrinsic molecular subtypes (
PAM50
)
Intrinsic molecular subtypes (
RIMSPC
)
TNBC (IHC) and/or Basal-like (PAM50)
TNBC subtypes
This analysis is only available with
DNA microarrays data
(only Affymetrix™ data will be taken into account).
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
.
OUTPUT CORRELATION FIGURE
Choose one of the radio button to select which output figure you want to get as a result plot.
Have a sneak peak of each figure by clicking on following options available:
Hexbin polychrome
,
Hexbin monochrome
,
Scatter plot
.
Type of plot:
Hexbin polychrome
Hexbin monochrome
Scatter plot
Pearson's pairwise Hexbin polychrome
Pearson's pairwise Hexbin polychrome with LOESS regression
Pearson's pairwise Hexbin monochrome
Pearson's pairwise Hexbin monochrome with LOESS regression
Pearson's pairwise Scatter plot
Pearson's pairwise Scatter plot with LOESS regression
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Legend
IHC:
immunohistochemistry
PAM50:
Parker's instrinsic molecular subtypes
RIMSPC:
robust intrinsic molecular subtype predictors classification based on patients classified in the same subtype with the six molecular subtype predictors (3 SSPs + 3 SCMs)
RSCMC:
robust SCM classification based on patients classified in the same subtype with the three SCMs
RSSPC:
robust SSP classification based on patients classified in the same subtype with the three SSPs
SCM:
Subtype clustering model (SCMOD1, SCMOD2 or SCMGENE)
SSP:
single sample predictor (Sorlie's, Hu's or PAM50)
TNBC:
triple-negative breast cancer; tumours negative for oestrogen and progesterone receptors and epidermal growth factor receptor 2 (HER2), by means of IHC
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2010
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Last update
Dec 12, 2022
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