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Advantages:
• Time saving (fast, 24/7)• Standardisation of the gating process
• Improved reliability (reproducibility & accuracy) by removing the variability of manual gating
• Adapted to deep and complex gating strategies
• Automation of quality controls and outlier identification
MASS/FLOW CYTOMETRY DATA ANALYSIS AltraBio offers comprehensive services for flow and mass cytometry data analysis from gating to cross-sample analysis. To maximise the value of your experimental results and to speed up your process, AltraBio’s offer covers the entire data analysis workflow from discovery and diagnostic studies to optimization of population identification processes.
• Immunophenotyping• Identification of cell populations to diagnose
a disease and/or its evolution• Identification & description of populations
responding to a therapy• Identification of therapeutic targets
Too much data to deal with?
SPADE ViSNE
Gating by clustering & dimension reduction
FlowSOM
Too many samples to gate?
Automation of manual gating by machine learning approaches
FCS File +
manual gating
Train computer
Trained computer
You
FCS File
FCS File + auto
gating
Making sense of your Data
FCS File
OMICS DATA ANALYSIS AltraBio's team implements and develops state-of-the-art and innovative methods for all kinds of omics studies (genomics, transcriptomics, proteomics, …) in both preclinical and clinical contexts with the aim of caracterizing new models, molecular mecanisms/markers of pathology, biological ways of interest (oxydative stress, immune response,…), effect of treatments at different doses, microbiotes.
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CXCL8
NAMPTP1
G0S2CXCL8
CX3CR1
FCGR3B
ZNF331
CXCR2
PDE4B
MAFF
NAMPT
NR4A2
CREM
S100P
OAS1
BCL2A1
PTGS2
CMTM2
HBEGF GPR183
RGCC
PLAUR
MS4A6A
IDI1
PFKFB3LOC284454
SLC25A37
SLC2A3
HBM
IL1B
CXCL2
GIMAP4
HBD
OSM
CCR2
IDH1RAB10
KCTD12
B3GNT5
TNFSF10
BASP1
IL1R2
ZBTB21
RGS1
EEF1D
SMCO4
CD83
MXD1
MGAM
LITAF
TNFAIP3
AQP9
SAMSN1
CXCR4
MS4A6A
FGD2ALAS2
VCAN
AATBC
COPB2
ABCA1
BRE−AS1
IFI27TLR8
SFPQATF3
TNFAIP8L2
TMEM176B
FOSGOLGA8A
CD69
SON
ZFP36
FFAR2
CA1
RNF103
CDKN1CKLRF1
GPRASP1
GZMH
IFITM2
ALDH1A1
FGFBP2
JUN
NSUN5P1
CLU
LINC00936
POU2AF1
IGHM
/1.2
/1.5
x1.2
x1.5
/1.2/1.5/2 x1.2 x1.5LAIV:(D3 / D0)
TIV:
(D3
/ D0)
●
●
●
●
Non−significant (adjusted p−value>0.05)
Significant in LAIV:(D3 / D0)
Significant in TIV:(D3 / D0)
Significant in both
• Cutting-edge data analysis methodologies• Extensive quality controls• Tailor-made statistical analyses• Functional analysis / pathway identification• Biological interpretation• Comprehensive report • Visualisation tool to interact with your results
AltraBio’s added value●
●
●
●
● ●
●●
−20 −10 0 10 20
−30
−20
−10
010
20
PC1
PC2
01
02
03
0405
0607
08
09
10
11 12
13 15
19
20
21
22 24
●●
●
●
●●
● ●
−30 −20 −10 0 10 20
−30
−20
−10
010
20
PC3
PC2
01
02
03
0405
0607
08
09
10
1112
1315
19
20
21
22 24
−1.0 −0.5 0.0 0.5 1.0
−1.0
−0.5
0.0
0.5
1.0
PC1
PC2
●
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●
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●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
CD24
LRRC17
SPON2
DDX17
POSTN
SPINK5
CHI3L1
SERPINA3
ADH1B
ALDH1A3KRT23
SFN
APOD
IGFBP3
ITGB6
IVL
KRT5
KRT6AKRT6B
KRT15
KRT16
KRT17
KRT19
KRTDAP
LAMA3
LAMB3
LCN2
TACSTD2CEACAM6
PI3
SERPINB5
FXYD3KLK7
S100A14
RARRES1
S100A2
S100A8
S100A9
S100P
CCL11
C19orf33
ERAP2
MIR205HG
SLPI
SPRR1A
SPRR1B
SPRR2A
VCAM1
GPRC5A
FGFBP1
% v
aria
nce
05
1015
2025
●
TimePoint J14 J18
Zone Zone− Zone+
Donor no15 no16
PCA
P129_03_01S16_no15_J14
P129_04_01S16_no15_J14
P129_05_01S16_no15_J14
P129_06_01S16_no15_J14
P129_01_01S16_no15_J14
P129_02_01S16_no15_J14
P129_13_01S16_no15_J18
P129_15_01S16_no15_J18
P129_21_01S16_no16_J18
P129_20_01S16_no16_J18
P129_19_01S16_no16_J18
P129_22_01S16_no16_J18
P129_09_01S16_no16_J14
P129_10_01S16_no16_J14
P129_11_01S16_no16_J14
P129_07_01S16_no16_J14
P129_08_01S16_no16_J14
P129_12_01S16_no16_J14
P129_24_01S16_no16_J18
ZoneTimePointDonor
Donorno15no16
TimePointJ14J18
ZoneZone−Zone+
100 10097 100100 100
100 100100 99
9971
1007986
87
87
Hierarchical clustering
PBS
APB
S A
PBS
APB
S A
PBS
APB
S B
PBS
BPB
S B
PBS
BPB
S B
Non
e B
Non
e B
Non
e B
Non
e B
Non
e B
Non
e B
T1 A
T1 A
T1 A
T1 A
T1 A
T1 A
T1 B
T1 B
T1 B
T1 B
T1 B
T1 B
T2 A
T2 A
T2 A
T2 A
T2 A
T2 B
T2 B
T2 B
T2 B
T2 B
T2 B
T3 A
T3 A
T3 A
T3 A
T3 A
T3 B
T3 B
T3 B
T3 B
T3 B
T3 B
− SERPINB4− CASP14− CRNN− KRT77− INHBB− SLC40A1− TPX2− PTGS1− TNNC1− SERPINB12− HSD11B1− C1orf105− FAM83D− RARRES1− CA6− ACPP− GAN− SLC45A4− TMEM99− SLC16A10− ALOX12− SLC1A6− SLC46A2− C15orf59− TYRP1− NUAK1− HMGB2− HOXC6− MKNK2− ZNF395− SLC6A8− CLCA4− PTTG1− PFKP− NDUFA4L2− IGFBP3− ALDOC− FOS− DDIT4− EGLN3− CA9− P4HA1− IER3− LRMP− PGF− PPFIA4− PFKFB4− MT1X− SERPINE1− FUT11− NDRG1− ANKRD37− PFKFB3− C7orf68− ANGPTL4− PPP1R3C− ADM− KCTD11− TCN1− S100A7A− ANKRD30BL− SLC7A5− PHLDA1− CH25H− S100P− STC2− ECM2− PHGDH− EIF4EBP1− NUPR1− ASS1− RCN1− PSAT1− MOCOS− SHMT2− CBS− CADM1− BCHE− SERPINE2− SLC7A11− PSPH− TUBE1− CHAC1− HERPUD1− MARS− TARS− XBP1− AARS− ASNS− PCK2− YARS− PRSS23− IFI6− IFI27− IFITM3− ISG15− HLA−B− DDX60− IFITM1− IFI44− XAF1− MX1− IFIH1− IFIT1− IFIT3− IGFL1− SPINK6− PI3− SPRR4− SYNM− CHST2− KRT9− FABP4− EPRS− LOC100131261− TOP1− M6PR− USO1− HIST1H4C− TAOK1− MALAT1− SMC3− PVRL4− SFRS18− ANKRD11− SECISBP2− DNAJC1− LEPROT− TSPAN5− TAF1D− CCAR1− S100A7− S100A12− MMP10− MMP3− TCHH− SPRR3− C14orf34− DHRS9− HMGCS2− RPTN− ODC1− KRT17− SPRR2A− SPRR2G− C4orf19− LCN2− UPP1− RNASE7− KRT75
Heat-Maps
Volcano plots
Geneset enrichment
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CXCL8
G0S2
NAMPTP1
NAMPT
PTGS2
FCGR3B
CXCL8
NR4A2
RGS1
CX3CR1
CLC
ZNF331
PDE4B
BRE−AS1
S100P
PFKFB3
EGR2
CXCL2
HBEGF
PLAURMAFF
NR4A3
CXCR2
BCL2A1
NFIL3
IL1B
AREG
SLC2A3
OSM
CREM
ACSL1
EEF1D
GPR183
B3GNT5
BASP1
SLC25A37
GIMAP4
AQP9
CMTM2
MS4A6A
IDI1
HBM
CD83
RGS2
MXD1
SGK1
PROK2
CSRNP1
ZBTB21
HBD
OAS1
CCR2
IDH1CXCL1
TREM1
C5AR1
IL1R2
DENND2D
KCTD12
EGR3
SAMSN1
TNFRSF10C
LITAF
RAB10
ATG2A
ATF3
THBS1
PELI1
MGAM
ZNF267
ALAS2
JUN
HSD17B4
LTF
IRS2
RAB20
SELENOK
MS4A7
VCAN
MS4A6A
CLEC12A
ISCA1
MNDA
RNASE6
TP53INP2
RGCC
SGK223
FAM53C
MIR22HGGAPT
METTL7A
TRG−AS1
CD36USP15
SOD2
GIMAP1
TRIB1
TRIM58
SLC35A1
MPEG1
MRPS31
SMCO4
FKBP5
YTHDF3
IL7R
GNA13
VCAN
DUSP2
CLEC2B
SLC25A39
RTN1
STK38
LRRC8D
ELP3
IFIT2
RB1CC1
TES
EGR1
FOSB
CUL4A
PROSC
MYOF
LYZ
IFI27
RAB18
FAM208A
SLU7
AK2
HERC5
GLG1
SELENOH
ARHGEF6
MRFAP1
1
0.01
10−4
10−6
/1.2/1.5/2 x1.2 x1.5LAIV:(D7 / D0)
adju
sted
p−v
alue
● ●Non−significant (adjusted p−value>0.05) Significant in LAIV:(D7 / D0)
Pairwise comparisons
What we deliverWhat we need What we do
Generated Data
AltraBio’s workflow
From your own providers or from our partners
Biological questions
Implementation of biostatistical and biomathematical methodsState-of-the-art methods/Customized statistical models/Classifier analyses
Comprehensive reportAnalysis methods & results/Publication quality
images/Oral presentation of the reports
Access to WikiBioPathWeb interface for visualization of the results
Making sense of your Data
Making sense of your Data
A Cross-Sectional Study Assessing the Contributions of Body Fat Mass and Fat-Free Mass to Body Mass Index Scores in Male Youth Rugby Players. Gavarry O, Lentin G, Pezery P, … Sports Med Open. 2018 May 2; 4(1):17.
Antigen-Induced but Not Innate Memory CD8 T Cells Express NKG2D and Are Recruited to the Lung Parenchyma upon Viral Infection. Grau M, Valsesia S, Mafille J, … J Immunol. 2018 Apr 9. pii: ji1701698.
Observational study of potential risk factors of immersion pulmonary edema in healthy divers: exercise intensity is the main contributor. Boussuges A, Ayme K, Chaumet G, … Sports Med Open. 2017 Oct; 3(1):35.
Human Dermal Fibroblast Subpopulations Display Distinct Gene Signatures Related to Cell Behaviors and Matrisome. Nauroy P, Barruche V, Marchand L, … J Invest Dermatol. 2017 Aug; 137(8):1787-89.
MMP-7 is a predictive biomarker of disease progression in patients with idiopathic pulmonary fibrosis. Bauer Y, White ES, de Bernard S, … ERJ Open Res. 2017 Mar; 3(1).
How can we work together?Subcontracts
Hundreds of analyses performed with major pharmaceutical, biotechnology & cosmetics
companies
Collaborative projects
SME partner for your grant applications (ANR, La Ligue, FUI, H2020, …)
- PREDIVAC & MEMOIRE Consortia -
Why AltraBio?• 12 years of expertise in the implementation and
development of bioinformatic tools (hundreds analyses performed) for:‣ life science data analysis/mining in
immunology, oncology, dermo-cosmetology‣ biological interpretation of results‣ databases generation
• A multidisciplinary team (bioinformaticians/mathematicians and biologists/physicians)
• A step-by-step approach with unsupervised and supervised analysis to adapt the analysis process to your problem
• WikiBioPath & Cytautomaton, proprietary tools allowing you to interact with your results & automate the application of your gating strategies
• Time & cost effective services• Our disponibility and flexibility
Recent publications…
They already trust us
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