Frequently asked questions
1. Why TIPMaP is developed?
2. Information provided by TIPMaP
3. Species covered
4. List of Affymetirx platforms covered
5. List of 3' Affymetirx platforms not covered
6. Source for Affymetrix probe sequences and CDF files
7. Source for RefSeq transcript sequences
8. How are probes aligned to transcripts?
9. Steps to process gene expression data of your interest
10. Is it possible to process the data locally?
1. Why TIPMaP is developed?
TIPMaP is developed to exploit gene expression data from standard 3' Affymetrix arrays and predict transcripts which are differentially regulated or detected.
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2. Information provided by TIPMaP
TIPMaP provides
a. Differentially detected or regulated transcripts
b. Gene, protein, transcript details
c. Probe to transcript BLAST alignment results
d. Aids in the identification of splicing regulatory motifs and
e. Can be used for RNA structural analysis
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3. Species covered
TIPMaP can be used to re-analyze the gene expression data for human, mouse and rat species.
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4. List of Affymetirx platforms covered
Standard 3' gene expression arrays are covered. The list of platforms include
Human: Human genome focus, Human genome U133 plus 2.0, Human genome U133 A2, Human genome U133 A, Human genome U133 B, Human genome U95 Av2, Human genome U95 B, Human genome U95 C, Human genome U95 D, Human genome U95 E, HT Human Genome U133A, HT Human Genome U133B, Human X3P
Mouse: Murine Genome U74A v2, Murine Genome U74B v2, Murine Genome U74C v2, Mouse Genome 430A 2.0, Mouse Genome 430 2.0, Mouse Expression 430A, Mouse Expression 430B, HT Mouse Genome 430A, HT Mouse Genome 430B
Rat: Rat Genome U34 A, Rat Genome U34 B, Rat Genome U34 C, Rat Genome 230 2.0, Rat Expression 230A, Rat Expression 230B, HT Rat Focus, Rat Toxicology U34 and Rat Neurobiology U34 arrays
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5. List of 3' Affymetirx platforms not covered
Around 4 paltforms are not included either due to non availability of or modifications in CDF (Chip Definition Files). The platforms include Human genome U95, Human genome U133 PM, HT Mouse genome 430 PM and HT Rat 430 PM.
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6. Source for Affymetrix probe sequences and CDF files
Affymetrix probe sequences and CDF files are downloaded from Affymetrix support by product page. Link "http://www.affymetrix.com/support/technical/byproduct.affx?cat=exparrays".
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7. Source for RefSeq transcript sequences
The transcript sequences are downloaded from NCBI ftp site. Link "ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz".
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8. How are probes aligned to transcripts?
Probes are aligned to transcripts using BLAST (locally installed) 2.2.25+ version. Link "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/".
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9. Steps to process gene expression data of your interest
a. Go to Download section
b. Choose a GPL platform
c. Select one or more GSEs
d. Enter name and e-mail ID
e. Click submit
An automated mail will be sent to your mail, once the data is downloaded and processed.
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10. Is it possible to process the data locally?
Yes!
In the download section of the interface, a zip file is available with programs and sample data - using which data can be processed and analyzed in-house.
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