Gene expression databases for kidney epithelial cells - PubMed (original) (raw)

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Gene expression databases for kidney epithelial cells

Jennifer C Huling et al. Am J Physiol Renal Physiol. 2012.

Abstract

The 21st century has seen an explosion of new high-throughput data from transcriptomic and proteomic studies. These data are highly relevant to the design and interpretation of modern physiological studies but are not always readily accessible to potential users in user-friendly, searchable formats. Data from our own studies involving transcriptomic and proteomic profiling of renal tubule epithelia have been made available on a variety of online databases. Here, we provide a roadmap to these databases and illustrate how they may be useful in the design and interpretation of physiological studies. The databases can be accessed through http://helixweb.nih.gov/ESBL/Database.

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Figures

Fig. 1.

Fig. 1.

The transcriptomic database webpage presents the user with 2 options for accessing information: links to each of the 3 segment-specific databases individually by clicking on the appropriate database title (A) and a Basic Local Alignment Search Tool (BLAST) search of all 3 databases at once by inputting the amino acid sequence into the input box (B). The “Results” page will display all similar sequences from the transcriptomic databases and indicate which databases contain each matched transcript. (Note that to avoid scrolling, it may be necessary to increase screen resolution for this page and subsequent pages.)

Fig. 2.

Fig. 2.

Sample output of a BLAST search. The Results page gives a brief explanation, a diagram of the nephron for reference, and a summary table displaying the key results of the search. The table lists matches based on amino acid sequence and for each protein displays general information about the protein and about the protein's location. A: 3 columns highlighted correspond to each of the 3 segment-specific databases being searched. A green icon in a column means that the protein does appear in the corresponding database, and a red icon means the protein does not (determined if the Probe Set ID had a signal strength <0.2). The numbers beside each icon are the signal strengths. B: when the user holds the cursor over the word “view” a visual summary of the previous three columns is shown. The signal strengths are displayed over the correct nephron region. Each region is also shaded in blue, with darker blue shading corresponding to a higher signal level. IMCD, inner medullary collecting duct.

Fig. 3.

Fig. 3.

Transcriptomic database for the medullary thick ascending limb (TAL). The page provides a description of the methods used to collect the data and displays information for all of the Affymetrix Probe Set IDs found in the TAL. Each probe set ID is listed along with the associated protein name, gene symbol, accession number, Swiss-Prot number, and the fluorescent signal strength in the array readout. The database also includes the following features: the option to sort the database (A), a link to the BLAST search featured on the main page so that users can find a specific protein by amino acid sequence (B), a link that downloads the data into a spreadsheet (C), the Swiss-Prot function of the proteins visible by holding the cursor over the Swiss-Prot number (D).

Fig. 4.

Fig. 4.

IMCD Proteome Database contains the same features as the transcriptome databases (sorting options, BLAST search, downloadable data, and mouse-over Swiss-Prot functions). In addition, the name of each protein links the user to the “Protein Viewer,” which displays various features mapped along the length of the protein's amino acid sequence. The “Tech view” feature allows the user to find the correct reference with the appropriate description of the techniques used to generate the data.

Fig. 5.

Fig. 5.

Phosphoproteomic database for proximal tubule and other renal cortical membrane proteins. The page provides a sortable table of phosphorylation sites detected along with the accession number, official gene symbol, protein name, phosphopeptide sequence detected, and site assignment information. In addition the user is able to download all the data as a spreadsheet or a PDF file.

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