|
bc-GenExMiner version |
Date |
Main evolution |
Updated data |
No. new patients |
No. datasets |
New functionalities |
| DNA microarray |
RNA-seq |
DNA microarray |
RNA-seq |
| New |
5.1 |
2024/07/23 |
Softwares only
|
--- |
--- |
--- |
|
|
Apache, MySQL and PHP were updated, as well as various layout details. |
|
5.0 |
2023/06/28 |
All modules updated |
|
193 |
407 |
|
|
TNBC (IHC) subtypes analyses: now available for DNA microarrays and RNA-seq all patients, and unavailable for Affymetrix™. |
| TNBC subtypes have been redefined. |
--- |
Four subtypes are used instead of three, to be used in affected evaluations. |
| New TNBC cohorts have been added to database (DNA microarrays and RNA-seq). |
--- |
--- |
|
4.9 |
2022/12/12 |
Correlation module updated |
|
--- |
--- |
|
|
Targeted and chromosomal location analyses: two new figures are available (hexbin polychrome and monochrome). |
| Gene annotations updated |
530 |
--- |
|
4.8 |
2022/01/17 |
Correlation module updated |
|
|
|
|
|
All analyses: new clinical item added (nodal status). |
| Expression module updated |
All analyses: choice of figure type at the first step, access to statistical data (table and while mousing over figure) and calculation time improved. |
| All modules updated |
EMF downloadable figure file format replaced by SVG format, easier to handle to suit journal requirements. |
Gene annotations updated
|
2 877 |
miRNA have been removed from microarrays and RNAseq dataset. |
Cohort curated
|
|
--- |
- 291 |
TCGA dataset have been curated from patients not responding to our inclusion criteria. |
|
4.7 |
2021/06/28 |
New type of analysis added |
|
--- |
--- |
|
|
Prognostic analysis: TNBC (IHC) subtypes. |
| Correlation module updated |
Targeted and chromosomal location analyses: calculation time improved. |
| Prognostic module updated |
TNBC & Basal-like analysis: analysis results are two ways displayed: by subpopulation or by time-to-event endpoint. |
|
4.6 |
2021/04/08 |
Correlation module updated |
|
643 |
--- |
|
|
Targeted analysis: a gene list file can be uploaded as an input. |
Expression module updated
|
|
Targeted analysis: 3 populations criteria added: pathological tumor stage (only avalaible for TCGA data), Ki67 and BRCA1/2 mutation status.
Exhaustive analysis: 3 populations criteria added (see targeted analysis). |
Gene annotations updated
|
1 561 |
--- |
|
4.5 |
2020/06/22 |
Correlation module updated |
--- |
527 |
1 234 |
|
|
Targeted analysis: PR, ER/PR, PAM50, Basal-like/TNBC, and TNBC subtypes populations criterion added.
Exhaustive analysis: 8 populations criteria added + updated results display.
Chromosomal location analysis: 8 populations criteria added + updated results display. |
| Expression module updated |
Targeted analysis: 3 populations criteria added: nature of the tissue, TNBC subtypes and integrative clusters.
Exhaustive analysis: 3 populations criteria added (see targeted analysis).
Customised analysis: discretisation option added. |
| Prognostic module updated |
Targeted analysis: PR population criterion added, mixed choice rename to all, one event added and rename all event status to 'DMFS', 'OS' and 'DFS'.
Exhaustive analysis: one event added and rename all event status to 'DMFS', 'OS' and 'DFS' + updated results display.
Intrinsic molecular subtypes analysis: possibility to choose between 3 populations events: 'DMFS', 'OS' and 'DFS' + deep update of results display.
Basal-like & TNBC analysis: one event added and rename all event status to 'DMFS', 'OS' and 'DFS' + updated results display (exhaustive event status analysis done). |
|
4.4 |
2019/12/09 |
Correlation module updated |
--- |
--- |
--- |
|
|
Targeted analysis: correlation analyses of up to 20 genes can be performed at one time. |
| Expression module updated |
Two new populations criteria have been added: histological types and P53 status.
Three new types of figure have been added: bee swarm, violin and raincloud plots.
Customised analysis: new gene expression data added (Affymetrix™, Metabric, TCGA, SCAN-B). |
| Prognostic module updated |
Targeted analysis: two versions of Kaplan-Meier curve are available (with or without tick marks). |
Gene annotations updated
|
830 |
--- |
|
4.3 |
2019/07/05 |
New cohorts have been added to database (DNA microarrays and RNA-seq).
|
--- |
4 305 |
4 712 |
|
|
--- |
| 4.2.1 |
2019/06/18 |
Expression and correlation modules updated
|
--- |
--- |
--- |
|
--- |
Figure files available in EMF format. |
| 4.2 |
2019/01/09 |
All modules updated
|
--- |
--- |
--- |
|
--- |
Automatic dropdown list of stored gene symbols.
Help for choosing Affymetrix™ probes by using the gene symbol with several options (median, highest ou JetSet probe). |
Prognostic module updated
|
Discretisation options added. Figure files available in EMF format. |
Gene annotations updated
|
1 354 |
--- |
| 4.1 |
2017/12/14 |
Gene annotations updated
|
4 823 |
--- |
--- |
|
--- |
--- |
| 4.0 |
2016/03/30 |
Expression module added
|
--- |
--- |
--- |
|
--- |
Expression analyses: targeted, exhaustive and customised |
New type of analysis added
|
|
Prognostic analysis: Basal-like and/or TNBC
Targeted correlation analysis: Basal-like and/or TNBC |
| 3.2 |
2015/09/04 |
Gene annotations updated
|
3 441 |
--- |
--- |
|
--- |
--- |
| 3.1 |
2014/12/11 |
New cohorts have been added to database
|
--- |
2 486 |
--- |
|
--- |
--- |
| Gene annotations updated
|
3 829 |
--- |
--- |
|
--- |
--- |
| 3.0 |
2014/03/07 |
New type of figure added
|
--- |
--- |
--- |
|
--- |
Box and whiskers plot figure corresponding to molecular subtype gene-expression map |
| 3.0 |
2012/02/15 |
Correlation module added
|
--- |
--- |
--- |
|
--- |
Correlation analyses: targeted, exhaustive and by chromosomal location |
| 2.1 |
2011/08/01 |
Gene annotations updated
|
637 |
--- |
--- |
|
--- |
--- |
| 2.0 |
2011/01/26 |
New type of analysis added
|
2 320 |
--- |
--- |
|
--- |
Prognostic analysis: molecular subtype |
| 1.1 |
2010/08/02 |
New cohorts have been added to database
|
1 359 |
336 |
--- |
|
--- |
--- |
| 1.0 |
2010/02/05 |
bc-GenExMiner v1.0 launching
|
1 325 |
--- |
--- |
|
--- |
Prognostic analyses: targeted and exhaustive |
Legend 
|
| DFS: | disease-free survival | | DMFS: | distant metastasis-free survival | | ER: | oestrogen receptor by IHC | | IHC: | ImmunoHistoChemistry | | OS: | overall survival (any relapse or death) | | PAM50: | Parker's instrinsic molecular subtypes | | PR: | progesterone receptor by IHC | | TNBC: | triple-negative breast cancer; tumours negative for oestrogen and progesterone receptors and epidermal growth factor receptor 2 (HER2), by means of IHC | | Updated data: | number of updated gene symbols and probesets |
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