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COMPARE, DTP public data
Skip Compare Site Nav
LOADING
COMPARE SITE NAVIGATION
CONFIGURE A SEARCH
SEARCH RESULTS
STANDARD COMPARE
GRID COMPARE
REQUIRE, USE OR IGNORE CELL LINES
UPLOAD SUPPLIER REPORT
IOA NSC SET
LOGOUT/RESET
RESET (if LOGOUT doesn't work)
Important information about GIPRCNT and Important Information about COMPARE correlations
GIPRCNT
The reponse values in the NCI60 concentration/response screening assay are the count of remaining cells as a percentage of the count of starting cells. By convention these are reported as "GIPRCNT." The "GI" does NOT stand for "G"rowth "I"nhibition.
COMPARE correlations
The sign of the mathematical correlation between two sets of cell line data will be "flipped" if the two sets of data have different "directionality."
"Forward" directionality means that larger numerical values are associated with either greater potency of a compound in the screen or greater expression (quantity or activity). The latter is the case for most data from expression (quantity or activity) studies of the NCI60 cell lines.
"Inverse" directionality means that smaller numerical values are associated with either greater potency of a compound in the screen or greater expression. The former is the case for most NCI60 compound screening data.
Most compound screening results from the NCI60 screen are "inverse." They report compound concentrations as the log10 transform of the concentration in the assay. This applies to the concentration/response data and the endpoint values (GI50, TGI, LC60) that are interpolated from the concentration/response data.
Conversely, most expression assay data from the NCI60 cell lines are "forward." Greater numerical values indicate greater quantity or activity.
The sign of a mathematical correlation is flipped so that the interpretation of a positive COMPARE correlation between NCI60 cell line screening results and expression measurements is: Increasing potency correlates with increasing expression.
To reflect this interpretation visually, the convention for meanGraph presentations of NCI60 screening data is to flip the X axis of the meanGraph so that smaller concentrations are to the right of larger concentrations. The visual interpretation is that more potent compounds (or more sensitive cell lines) have bars further to the right than less potent compounds (or less sensitive cell lines. Expression data are rendered with a standard X axis. Bars for screening results that are positively correlated with expression data will tend to have bars in the same relative directions.
Overview of using the web site
COMPARE Site Navigation
INFO
An overview of using COMPARE web sites.
SEARCH
Search available Cell Line Data Sets. The available searches could include compound screening data or various types of molecular expression data depending on what data sets underlie this version of COMPARE.
RESULTS OF MOST RECENT SEARCH
Return to the search results from the most-recent search.
STATUS
Information about the data that underlie this version of COMPARE. NOT YET AVAILABLE IN PRODUCTION.
REQUIRE USE IGNORE
By default COMPARE will work with data for all available cell lines. This means that all cell lines are set to 'USE' status. Optionally, the status of selected cell lines can be set to 'IGN' (IGNored) status which means that they will not be used for any operations (Any 'IGN'ordered cell lines will not be retrieved when fetching data and they will not be considered when COMPARE calculations being run on data.) Optionally, cell lines can be set to 'REQ' (REQuired) which means that all cell lines in the cell line data set will be ignored UNLESS there are data for all of the cell lines set to 'REQ' status.
UPLOAD
Users can upload sets of cell line data and use them alongside the data that underlie this version of COMPARE. NOT YET AVAILABLE IN PRODUCTION.
AD HOC
Sets of COMPARE correlations can be calculated for pairs of specified cell line data sets. NOT YET AVAILABLE IN PRODUCTION.
LOGOUT
End this COMPARE session. Can also be used to try to reset a session if COMPARE has become unresponsive.
RECOVER FROM FREEZE
RECOVER FROM FREEZE
If LOGOUT doesn't restore an unresponsive site then this link triggers a final attempt.
Often-encountered Options
Download as Excel
Export the current data table in .xls format.
Download as csv
Export the current data table in .csv format.
Export Image
Export the graphic in .png format.
Searching COMPARE Data
SEARCH AS CONFIGURED BELOW
This will search available cell line data sets using the search criteria specified in the search forms. This could include search criteria for multiple different data types depending on which data sets underlie this version of COMPARE.
CLEAR SEARCH
Clear previous search results and all search criteria.
NO ICON
DEMONSTRATION SEARCH
A search will be configured and run using representative criteria for all available cell line data sets. If you run a demonstration search you can return to the SEARCH page to see representative search terms specified for the types of data which underlie this version of COMPARE. This will CLEAR all search results and all search criteria before executing.
NO ICON
COMPOUND SAMPLE SEARCH
A search will be run using a random set of 200 NSC in the cell line screening data that underlie this version of COMPARE. This will CLEAR all search results and all search criteria before executing.
NO ICON
APPROVED AND INVESTIGATIONAL SET
A search will be run for any NSC in the cell line screening data that underlie this version of COMPARE that are in the DTP IOA set of approved and investigational clinical agents. This will CLEAR all search results and all search criteria before executing.
Search Critiera
NSC Compound Data
nscTextArea
Type or copy/paste lists of NSC numbers. All numbers are assumed to be from the NSC 'S' series. Anything other than numbers will be ignored.
nsc autoComplete
After three characters are entered possible matching NSC will be shown. Select a suggested NSC to add it to the nscTextArea.
compoundNameTextArea
Type or copy/paste lists of compound names. These are the assigned names
compoundName autoComplete
After three characters are entered possible matching compoundNames will be shown. Select a suggested compoundName to add it to the compoundNameTextArea.
expIdTextArea
EXPLANATION of expIdTextArea
MicroArray Data by Gene Symbol or ProbeSetId
geneSymbolTextArea
Type or copy/paste lists of HUGO gene symbols.
geneSymbol autoComplete
After three characters are entered possible matching gene sysmbols will be shown. Select a suggested geneSymbol to add it to the geneSymbolTextArea.
geneTitle autoComplete
After three characters are entered possible matching gene titles (from Affymetrix) will be shown. Select a suggested geneTitle to add the corresponding geneSymbol to the geneSymbolTextArea.
probeSetIdTextArea
Type or copy/paste lists of Affymetrix probeSetIds.
probeSetId autoComplete
After three characters are entered possible matching gene probeSetIds (from Affymetrix) will be shown. Select a suggested geneTitle to add the corresponding probeSetId to the probeSetIdTextArea.
MicroRNA Data by miR
miRTextArea
Type or copy/paste lists of miRbase miRids.
miR autoComplete
After three characters are entered possible matching miRs will be shown. Select a suggested miR to add it to the miRTextArea.
All Molecular Targets by MoltId
moltIdTextArea
Type or copy/paste lists of DTP moltIds.
User Uploaded Data
lookupWordTextArea
EXPLANATION of lookupWordTextArea
Search Results
Collecting and Acting On Search Results
Configure and Fetch NCI60 Data
Explanation
SET
Replace any previouly-collected cell line data sets with the current selection.
APPEND
Append the current selected cell line data sets to the current collection.
STACKED DATA, limit 2000
Cell line values for all collected cell line data sets with a single cell line value per row.
MEAN GRAPHS, limit 25
A graphical presentation of the cell line data for the collected cell line data sets using the DTP MeanGraph format.
HEAT MAP, limit 200
A graphical presentation of the cell line data for the collected cell line data sets as a heat map.
ALL PLOTS, limit 25
A graphical presentation of the cell line concentration-response data for the collected cell line data sets.
The Return from Fetch NCI60 Data
Configure and Run Batch COMPARE
Explanation
SET
Replace any previouly-collected cell line data sets with the current selection.
APPEND
Append the current selected cell line data sets to the current collection.
Configure Batch COMPARE
EXPLANATION
The Return from Batch COMPARE
Details
STACKED
Configure and Run Grid COMPARE
A grid COMPARE returns a grid of COMPARE correlations, one cell for each possible pairwise combination of data sets specified as rows and columns. There is a limit of 1000 rows and 1000 columns.
ROWS SET
Replace any previouly-collected cell line data sets for the grid rows with the current selection.
ROWS APPEND
Append the current selected cell line data sets to the current collection of cell line data sets for grid rows.
COLUMNS SET
Replace any previouly-collected cell line data sets for the grid columns with the current selection.
COLUMNS APPEND
Append the current selected cell line data sets to the current collection of cell line data sets for the grid columns.
Configure Grid COMPARE
EXPLANATION
The Return from Grid COMPARE
Details
STACKED
GRID
application: publiccompare version: v20220411 build: 2022-04-26 19:02 compareUMLversion: 20220411_postgres
loggedUser: PUBLIC D: false A: false S: false
AVGDATAONLY: false NSCONLY: false
doIt
PNG format Graphic
Right click on image to copy/save
ESC to close
AdHoc Reporting
ESC to close
Brushed Nodes
ESC to close
brushedDrugTargets
brushedNscs
brushedGeneSymbols
brushedIdentStrings
Histogram Bar Elements
ESC to close
barObjects:
MEAN GRAPHS
HEAT MAP
TEST EXCEL STREAM
VALUES
DELTA
SHOW/HIDE TEXT
HTML
fakeCol1
fakeCol2
fakeCol3
No records found.
CONCENTRATION/RESPONSE
nscCompound
drugName
logHiConc
concUnit
expId
assayTime
cellPanel
cellLine
concentration
countPctCtrl
meanPctCtrl
stddevPctCtrl
No records found.
LABEL NODES BY TARGET, NSC OR DRUG NAME
ESC to close
APPLY SELECTED LABELS
Pick Targets
Pick NSC
Pick DrugNames
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LEGENDS BY TARGET
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APPLY
LEGEND
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FILTERS BY TARGET
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APPLY SELECTED FILTERS
FILTER
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HIGHLIGHTS BY TARGET
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APPLY
HIGHLIGHTS
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