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(eCALIBRATOR)
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AN INTERACTIVE WEB-BASED TOOL WHICH CAN BE USED TO PERFORM COMPARATIVE ANALYSIS ON YOUR OWN DATA OR BY QUERYING THE EUCALYPTUS BIOTIC STRESS DATABASE FOR GENE AND TRANSCRIPT DATA-SETS.

eCALIBRATOR OFFERS TWO COMPARATIVE INTERACTIVE ANALYSIS TOOLS: VENN PLOT AND HC PLOT.

VENN PLOT - IDENTIFIES THE INTERSECTS FOR UP TO SIX DATA-SETS AND DISPLAYS THE RESULTS VISUALLY BY DRAWING AN INTERACTIVE VENN DIAGRAM BY UTILISING A JQUERY JAVASCRIPT PLUG-IN CALLED JVENN DEVELOLPED BY Bardou et al. (2014).

HC PLOT - PERFORMS HIERARCHICAL CLUSTERING BY UTILISING A PYTHON SCRIPT TO PERFORM HIERARCHICAL CLUSTERING WHILE VISUALISING THE RESULT THROUGH AN INTERACTIVE JAVASCRIPT PLUG-IN CALLED InCHlib DEVELOLPED BY Skuta, Bartunek, and Svozil. (2014).

TOOL SELECTION
HC PLOT

VENN PLOT

CHOOSE BETWEEN TWO COMPARATIVE INTERACTIVE TOOLS.

HC PLOT: CHOOSE THIS OPTION TO USE THE INTERACTIVE HIERARCHICAL CLUSTERING TOOL

VENN PLOT: CHOOSE THIS OPTION TO USE THE INTERACTIVE VENN/ EDWARDS DIAGRAM DRAWING TOOL


DATA INPUT
BROWSE DATABASE
PROVIDE OWN DATA
BROWSE DATABASE
PROVIDE OWN DATA

CHOOSE BETWEEN TWO DATA INPUT METHODS FOR THE VENN PLOT INTERACTIVE TOOL.

BROWSE DATABASE: CHOOSE THIS OPTION TO QUERY THE EUCALYPTUS INTERACTIVE EXPLORER DATABASE THROUGH VARIOUS FILTERING AND DATASET SELECTION OPTIONS.

PROVIDE OWN DATA: CHOOSE THIS OPTION TO PROVIDE YOUR OWN DATA BY COPY-PASTING INTO THE RELEVANT TEXT BOXES.

SIX OPTIONS ARE AVAILABLE TO FILTER THE EUCALYPTUS PLANT PATHOGEN INTERACTION DATASETS WITHIN THE EUCALYPTUS INTERACTIVE EXPLORER DATABASE.

TRANSCRIPT/GENE: CHOOSE TO RETRIEVE EUCALYPTUS IDS FOR EITHER TRANSCRIPTS OR GENES.

DIFFERENTIAL EXPRESSION/ EXPRESSION: THE DATA CONTAINED WITHIN THE EUCALYPTUS INTERACTIVE EXPLORER DATABASE IS TRANSCRIPTOMIC DATA AND WILL BE RETRIEVED BASED ON FILTERING THIS DATA USING THRESHOLDS WHICH WILL ALTER THE AMOUNT OF RETRIEVED TRANSCRIPT/GENE IDS. THIS OPTION FACILITATES THE CHOICE TO FILTER ON FOLD-CHANGE OR FPKM RESPECTIVELY.

INEQUALITY: THIS OPTION FACILITATES THE DIRECTION DESIRED (IF APPLICABLE) TO FILTER THE TRANSCRIPTOMIC DATA ON FOLD-CHANGE OR FPKM RESPECTIVELY.

THRESHOLDS: THIS OPTION ALLOWS THE INPUT OF A SPECIFIC THRESHOLD FOR FILTERING BASED ON THE CHOICE OF THE DIFFERENTIAL EXPRESSION/ EXPRESSION AND INEQUALITY OPTIONS CHOSEN. IF 'BOTH' WAS CHOSEN FOR THE INEQUALITY OPTION, THEN AN UPPER AND LOWER THRESHOLD MUST BE SPECIFIED.

Q-VALUE: THIS OPTION SPECIFIES THE SIGNIFICANCE THRESHOLD TO FILTER DIFFERENTIALLY EXPRESSED DATA LISTS BASED ON THE Q-VALUE GENERATED AFTER MULTIPLE TEST CORRECTION WITH A BENJAMINI-HOCHBERG CORRECTION.

DATASET QUERIES NUMBER: THIS OPTION SPECIFIES THE NUMBER OF DATABASE QUERIES USED TO GENERATE THE REQUIRED NUMBER OF DATASETS TO COMPARE WHEN CALCULATING THE INTERSECTS USED TO DRAW THE VENN/EDWARDS DIAGRAMS RESPECTIVELY. AN OPTION OF 2 WOULD PRODUCE A 2-WAY VENN/EDWARDS DIAGRAM RESPECTIVELY.

NUMBER OF INPUT DATASETS
2
3
4
5
6

VENN AND DATABASE OPTIONS

SELECT GENE OR TRANSCRIPT DATA

SELECT TYPE OF EXPRESSION DATA

SELECT TYPE OF INEQUALITY

SELECT FOLD-CHANGE/EXPRESSION THRESHOLDS

SELECT Q-VALUE THRESHOLDS

SELECT DATA BASE QUERIES

2
3
4
5
6

CHOOSE BETWEEN FOUR DATA INPUT METHODS FOR THE INTERACTIVE HIERARCHICAL CLUSTERING & HEATMAP PLOTTING TOOL.

HCPLOT NO DATA: CHOOSE THIS OPTION TO CHOOSE HIERARCHICAL CLUSTERING WITH NO META-DATA.

HCPLOT COLUMN AND ROW META-DATA: CHOOSE THIS OPTION TO TO CHOOSE HIERARCHICAL CLUSTERING WITH BOTH COLUMN AND ROW META-DATA.

HCPLOT COLUMN META-DATA: CHOOSE THIS OPTION TO TO CHOOSE HIERARCHICAL CLUSTERING WITH BOTH COLUMN META-DATA.

HCPLOT ROW META-DATA: CHOOSE THIS OPTION TO TO CHOOSE HIERARCHICAL CLUSTERING WITH BOTH ROW META-DATA.

CLUSTERING OPTIONS

CLUSTERING ON: CHOOSE TO PERFORM CLUSTERING ON EITHER ROW OR ROW & COLUMN.

ROW DISTANCE: CHOOSE THE ROW DISTANCE ALGORITHYM.

ROW LINKAGE: CHOOSE THE LINKAGE ALGORITHYM USED TO SORT THE ROW DISTANCE MATRIX.

COLUMN DISTANCE: CHOOSE THE COLUMN DISTANCE ALGORITHYM.

COLUMN LINKAGE: CHOOSE THE LINKAGE ALGORITHYM USED TO SORT THE COLUMN DISTANCE MATRIX.

NORMALISE DATA: IF DATA BEING ANALYZED CONTAINS DIFFERENT SCALES BETWEEN COLUMNS, CHOOSE THIS OPTION TO NORMALISE TO A SCALE BETWEEN 0 AND 1.

WRITE ORIGINAL DATA TO HEATMAP: AVAILABLE IF NORMALISATION = YES; CHOOSE TO DISPLAY HEATMAP WITH NORMALISED DATA OR ORIGINAL DATA.

CHOOSE DATABASE BROWSE OPTIONS AND CLUSTERING OPTIONS FOR THE HC PLOT TOOL DATABROWSE OPTION.

CLUSTERING OPTIONS

CLUSTERING ON: CHOOSE TO PERFORM CLUSTERING ON EITHER ROW OR ROW & COLUMN.

ROW DISTANCE: CHOOSE THE ROW DISTANCE ALGORITHYM.

ROW LINKAGE: CHOOSE THE LINKAGE ALGORITHYM USED TO SORT THE ROW DISTANCE MATRIX.

COLUMN DISTANCE: CHOOSE THE COLUMN DISTANCE ALGORITHYM.

COLUMN LINKAGE: CHOOSE THE LINKAGE ALGORITHYM USED TO SORT THE COLUMN DISTANCE MATRIX.

NORMALISE DATA: IF DATA BEING ANALYZED CONTAINS DIFFERENT SCALES BETWEEN COLUMNS, CHOOSE THIS OPTION TO NORMALISE TO A SCALE BETWEEN 0 AND 1.

WRITE ORIGINAL DATA TO HEATMAP: AVAILABLE IF NORMALISATION = YES; CHOOSE TO DISPLAY HEATMAP WITH NORMALISED DATA OR ORIGINAL DATA.

DATA BROWSE OPTIONS

SELECT GENE OR TRANSCRIPT: SELECT EITHER GENE OR TRANSCRIPT TO RETRIEVE EITHER GENE OR TRANSCRIPT DATA.

SELECT TYPE OF EXPRESSION: SELECT EITHER FOLD-CHANGE OR FPKM TO RETRIEVE EITHER DIFFERENTIALLY EXPRESSED (LOG2 FOLD-CHANGE) OR EXPRESSION DATA (FRAGMENTS PER KILOBASE OF TRANSCRIPT PER MILLION MAPPED READS).

SEED DATASETS: SELECT A SEED DATASET TO BE RETRIEVED FROM THE DATABASE; THE SEED DATASET IS USED TO RETRIEVE A FILTERED LIST OF GENES OR TRANSCRIPTS WHICH CAN BE COMPARED ON AN EXPRESSION OR DIFFERENTIAL EXPRESSION LEVEL.

SELECT TYPE OF EXPRESSION: SELECT EITHER FOLD-CHANGE OR FPKM TO RETRIEVE EITHER DIFFERENTIALLY EXPRESSED (LOG2 FOLD-CHANGE) OR EXPRESSION DATA (FRAGMENTS PER KILOBASE OF TRANSCRIPT PER MILLION MAPPED READS).

INEQUALITY: THIS OPTION FACILITATES THE DIRECTION DESIRED (IF APPLICABLE) TO FILTER THE RETRIEVED DATA ON FOLD-CHANGE OR FPKM RESPECTIVELY.

THRESHOLDS: THIS OPTION ALLOWS THE INPUT OF A SPECIFIC THRESHOLD FOR FILTERING BASED ON THE CHOICE OF THE DIFFERENTIAL EXPRESSION/ EXPRESSION AND INEQUALITY OPTIONS CHOSEN. IF 'BOTH' WAS CHOSEN FOR THE INEQUALITY OPTION, THEN AN UPPER AND LOWER THRESHOLD MUST BE SPECIFIED.

Q-VALUE: THIS OPTION SPECIFIES THE SIGNIFICANCE THRESHOLD TO FILTER DIFFERENTIALLY EXPRESSED DATA LISTS BASED ON THE Q-VALUE GENERATED AFTER MULTIPLE TEST CORRECTION WITH A BENJAMINI-HOCHBERG CORRECTION.

HC PLOT AND DATABASE OPTIONS

SELECT
GENE OR TRANSCRIPT DATA

SELECT
TYPE OF EXPRESSION DATA

SELECT
SEED FOR GENE DIFFERENTIAL EXPRESSION DATASET

SELECT
SEED TRANSCRIPT DIFFERENTIAL EXPRESSION DATASET

SELECT
SEED GENE EXPRESSION DATASET

SELECT
SEED TRANSCRIPT EXPRESSION DATASET

SELECT
TYPE OF INEQUALITY

SELECT
EXPRESSION THRESHOLDS

SELECT Q-VALUE THRESHOLDS

ADD DATA SETS
HIERARCHICAL CLUSTERING

ROWS
HCPLOT HEATMAP DESIGNER
ADDITION OF DATASETS TO COMPARE TO SEED DATASET

DATA INPUT METHOD

NO META-DATA


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