High Confident Human Glomerulus Proteome identified both by Mass Spectrometry- and Antibody-based Proteomics Beta
This interface is preliminary.
This database (High Confident Human Glomerulus Proteome) was compared glomerular proteome by antibodies and mass spectrometer.
Proteins identified in both, is treated as a proteome data set with a high reliability than ever.
Providing a data set of antibodies and proteomics mass spectrometry proteomics, were compared with each other.
It compared Gene symbol.
Converts to what Gene Nomenclature Committee (HGNC) approved on March 21, 2014, Gene symbol was unified.
Mass spectrometry proteomics dataset
For comparison data of mass spectrometer proteomics, we used basis of LC-MS/MS human glomerulus was analyzed by HKUPP.
It data contain 6,686 proteins derived from 2,725 genes identified by Spectrum Mill.
We were convertible to "HGNC Approved" is Gene symbol was the 6,686 proteins derived from 2,725 genes.
We were used this 2725Gene symbol as a mass spectrometer dataset.
Antibody proteomics dataset
For comparison data of Antibody proteomics, we used the image and Intensity of immunohistochemistry of human glomeruli that are published (version 13) Human Protein Atlas.
There is 21984 antibodies 16621 genes, and subject are 16383genes 2064antibodies was tested on glomerulus.
Convertible Gene symbol to "HGNC Approved" were 16019 gene symbols.
HPA determination of the staining intensity High, Medium, Low, and Not detected were change to staining intensity scores of 3, 2, 1, 0.
And Each gene symbols gave the average of the staining intensity score.
For determination of glomerular expression, Positeve as staining scores given to Gene symbol is case of 1 or more, and Negative as less than 1.
Finally, for comparison dataset contains Glomerular positive is 7986 genes, negative is 8033 genes.
Result of Comparison
As a result of the comparison, Gene symbol common to antibodies and proteomics mass spectrometry proteomics is a proteomics data with high reliability.
Antibody Proteome data
Mass spectrometry Proteome data
Detected Gene symbols
How to Use
You can select the checkbox as proteome data part.
Venn diagram is divided into 5 parts of the result of the comparison of the Mass spectrometer and Antibody proteomics is shown.
For example, if you check only the check box of the Mass + Antibody +(Indicate only red part on Venn diagram), only proteomic data of high reliability to search.
The search is determined from Protein name or Gene symbol in selected Target Area.
Current version is possible to search only a single word.
If Search Word is blank, result will display all Gene symbol of including in Target Area.
Next describe Setting in Operation and item, you can search from only Gene symbol or only protein name.
SubmitFThis button sends condition by the Search Word and Target Area to the server, and get search results.
ResetFThis button is restore to initial state the Search Word and Target Area.
SettingFThis button is possible to change the operation settings of the search.
* Display Results per Page: number of the list to be displayed on one screen.
* Display Target Item: selection of items to include in the search results.
* Search Word Target: Search Word will search from each items.