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Example Data
Introduction PDF Print

Description of the sample data

The algorithms provided on this site require seed data of known genes that are a target of a specific transcription factor of interest. We provide sample data that represent names from known transcription factor targets  for each of the following individual arbitrarily chosen transcription factors, namely NFkB, E2F, ETS1, HIF-1, HNF4, c-Myc. The seed data is given as ensemble gene identifiers.

Data Sources
The data of known transcription factors come from review papers. We used the following sources: NFkB [1],  E2F [2;3], ETS1 [4;5], HIF-1 [6], HNF4, c-Myc [7].


References

  1. Wu JT, Kral JG. The NF-kappaB/IkappaB signaling system: a molecular target in breast cancer therapy. J.Surg.Res.; 123: 158-69.2005
  2. Bracken AP, Ciro M, Cocito A, Helin K. E2F target genes: unraveling the biology. Trends Biochem.Sci.; 29: 409-17.2004
  3. Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res.; 17: 1550-61.2007
  4. Sementchenko VI, Watson DK. Ets target genes: past, present and future. Oncogene.; 19: 6533-48.2000
  5. Hollenhorst PC, Shah AA, Hopkins C, Graves BJ. Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev.; 21: 1882-94.2007
  6. Semenza GL. Targeting HIF-1 for cancer therapy. Nat.Rev.Cancer.; 3: 721-32.2003
  7. Fernandez PC, Frank SR, Wang L, Schroeder M, Liu S, Greene J, Cocito A, Amati B. Genomic targets of the human c-Myc protein. Genes Dev.; 17: 1115-29.2003

 

 
Example Data c-myc PDF Print

This contatians a list of c-myc targets that might be used as an input to find similar genes. You may apply the Copy/Paste function of your Browser to use these IDs as input for the Gene IDs field in the input form.

For many more examples please have a look at the documentation section.

Read more...
 
HNF 4 example seed PDF Print

HNF4 example seed data:


ENSG00000057593

ENSG00000091513

ENSG00000100197

ENSG00000117054

ENSG00000126218

ENSG00000129214

ENSG00000130427

ENSG00000138823

ENSG00000173531

ENSG00000185010

ENSG00000198610

 

 
HIF1a example seed PDF Print

The list contains gene identifiers of known HIF1a target genes that might be used a seed.

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Example Data ETS1 PDF Print

This contains a list of ETS1 target genes that might be used as a seed:

Read more...
 
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