LCDIP help and instructions
Source naming follows the general convention of the publication's first author's last name with a suffix describing the data type: ma - mRNA microarray, snp - SNP microarray, rt - RT-qPCR, cgh - aCGH, mi - microRNA microarray, me - methylation microarraySearching LCDIP meta-data and data using the Search page and standardized meta-data terms:
1) Mouse over meta-data group terms (grey) to view meta-data terms.
2) Expand and click to select term of interest.
3) Use the 'Ctrl' or the 'Shift' keys to select/de-select multiple terms.
4) Some fields e.g.,Year of PUbllication, Age require user data input.
5) Use the 'ClearAll', or 'Clear' for each term group to make modifications on the terms selection.
6) Confirm the values entered (e.g., Age)
7) Select one output/export format in the left panel:
-Display; search results metadata shown in a new tab
-Download to file (meta-data + Gene Expression); tab-delimited output. Add up to 50 gene symbols in the Gene list box under the Expression group term to obtain gene specific data.
If no gene symbol is provided, all expression data is returned.
Additional gene and probe annotation are provided via hyperlinks to the following resources:
I2D - Interologous Interaction Database ophid.utoronto.ca
GeneCards The human gene compendium http://www.genecards.org
GeneAnnot Affymetrix probeset annotation http://genecards.weizmann.ac.il/geneannot/
Please note: Gene Expression Search may take several minutes to complete .
-Download to GeneE file; tab-delimited output file in the format compatible with viewing using the Broad Institute's GeneE matrix visualization software (http://www.broadinstitute.org/cancer/software/GENE-E/download.html)
If no gene symbol is provided, complete expression data is returned.
Gene Expression Search may take several minutes to complete.
8) Click the Submit button
9) The search results would be for samples annotated for all selected terms (intersection).
To refine the search or choose specific terms you may check the Statistics page for meta-data availability across datasets.
Search results may contain additional meta-data obtained from the original publication. Please note that the additional meta-data was not curated or standardized.
Download page:
Download the raw data, preprocessed data and meta-data for LCDIP datasets.
Statistics page:
1) View all the datasets publication year and PubMed link
Under View Stats for...
1) Summary of Available Data: view a summary table of all meta-data in LCDIP
2) Use any of the 26 quick links to a preview the meta-data distribution for the selected meta-data term.
Login:
Login for admin use only.