Breast Cancer Gene-Expression Miner v5.0
(bc-GenExMiner v5.0)

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ANALYSIS
- CORRELATION
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TUTORIAL
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- EXPRESSION
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BACKGROUND
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- DATA ANALYSIS

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HOW TO CITE US?

Gene correlation analysis by chromosomal location

Enter input gene and choose one of the following options:

GENE EXPRESSION DATA

First, choose your gene expression data. Information about cohorts : microarrays or RNA-seq

Then fill the textbox with actualised* gene symbol.

*: see actualised web databases (e.g.: Ensembl, GeneCards, HGNC, NCBI Gene...)

DNA microarrays

All

(n = 10 872)

RNA-seq

All

(n = 4 421)

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 all DNA microarrays or all RNAseq data.
This option allows to explore triple-negative breast cancer (TNBC) (IHC) subtypes (LAR, MLIA, BLIA and BLIS):

LAR: luminal androgen receptor,
MLIA: mesenchymal-like immune-altered,
BLIA: basal-like immune-activated,
BLIS: basal-like immune-suppressed.

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

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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Breast Cancer Gene-Expression Miner v5.0(bc-GenExMiner v5.0)

Gene correlation analysis by chromosomal location

Breast Cancer Gene-Expression Miner v5.0
(bc-GenExMiner v5.0)