TUNiNG-BASE™
Start of analysis:
Snapshot
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Group Dataset name Type Array Ig NC Regist date Memo
Normalization :
Group centering :
Sample summary
Green
Red
Green & Red
Sample ID Sample name N Valid N Valid % Valid N Valid % Valid N Valid %
Distribution and PCA
Plot
Export
Reset
Exact match
Case sensitive
Sample ID
Log2
Unknown Protein/Gene
results
Group
Each
Intensity ≥
Intensity ⇵
(
× SD )
× (1.4826⋅MAD) )
&
Intensity ≥
&
Fold change ≥
←
Hit samples ≥
and
Basic intensity (%tile)
≤
Exhaustive search
results
Basic population
Variation targets
Sort:
Export
Clustering
Venn(Whole)
Venn(Individual)
Enrichment
Fig.s(Whole)
Fig.s(Targets)
N ID Gene/Protein
N Hits Intensity ≧ Fold change ≧ Hit samples ≧ Basic %tile ≧ Max basic
Geneset name Size
Enrichment analysis
Clear
Geneset name Size
Intensity ≥
max:
min:
N:
Fold change ≥
Hit samples ≥
Basic intensity (%tile)
≤
max:
min:
N:
Exhaustive
search
Set default
conditions
Group
Each
Test:
direction:
q-value ≤
fold change:
Volcano plot
Export
Clustering
Venn
Enrichment
Fig.s(Whole)
Fig.s(Targets)
N
N ID Gene/Protein Log(fc) P-value Q-value
This analysis is based on the results of "Variant search",
so please perform the "Variant/Pattern search" first.
Import geneset
Unknown genes
Example
Reset
Plot
Clustering
Enrichment
Distance:
Linkage:
Variation
Comparison
Pattern
Venn
GeneSet
Whole
Clustering
Gene list
Enrichment
Missing value:
class0:
0
class1:
0
Cross Validation
Machine Learning Model
Score
Logistic Regression
k Nearest Neighbors
Support Vector Machine
Random Forest
Gradient Boosting
Evaluation
Score
Accuracy
Precision
Recall
F1
Group
Each
Correlation:
Average ≥
Upper/Lower ≥
Upper,Lower p-tile:
Copy group pattern
Sort:
Export
Clustering
Venn
Enrichment
Fig.s (Box)
Fig.s(Scatter)
N ID Gene/Protein
Gene symbol
Gene set:
Enrichment
Reset
N ID Description Size Overlap P-value Q-value
Gene list of gene set
Plot
Clustering
Overlap only
N Symbol Description
Gene:
Sample:
Mutation:
Stop/Short
Point
Scale:
Low:
High:
Log2
View
Clear
Export
Submit
Gene Memo
New
Scale:
Clear
Open
Edit
Delete
Share
Snapshot date & time Analysis Title Memo
Update
Share selected analysis results with TFBase users in your organization.
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Normalization:
FMU normalization
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Summary
Quality Check
Plot intensity
Variation
Comparison
Pattern
Model to classify
Clustering
Venn diagram
Geneset
Mutation
Fig.s
Memo
Record
Export
Take a snapshot of the current analysis results.
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Title:
Memo: