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Automatic conversion of mixed input

You may provide input lists in various formats that might be mixed. Possible formats for the human example gene Mitogen-activated protein kinase 1, also known as MAPK1 are:

  • Ensembl Gene ID, e.g.:
  • Genes Entez ID of NCBI, e.g.:
  • Plain gene abreviation, e.g.:

 

Combined display of ranking

The results of the ranking according to the expression similarity can be combined with affinity statistics of transcription factors in the promotor regions of the genes at targetfinder.org. High affinities result in a low normalized affinityrank. Here you find a section ot the output of the filtering with a the transcription factor c-myc.  

Filtered Result

Transcription factor: MYCMAX_01

Affinityrank cut_off: 0.1

Maximum in Rank Liste: 500

Affinityrank less than 0.005 less than 0.01 less than 0.02 less than 0.05 less than 0.1

Rank Mean correlation Entrez Gene ID Other IDs Affinityrank
8 0.399 , , , , , , , 0.062107
17 0.362 , , , , 0.058653
40 0.33 , , , , 0.074670
49 0.322 , , , , , 0.046796
52 0.319 , , , , 0.058574
64 0.309 , , 0.003847
65 0.308 , , 0.095948
68 0.306 , , , , 0.040594
72 0.305 , , , , , , , 0.045383
75 0.302 , , , , , 0.002198
85 0.299 , 0.077104

 

Output lists are linked to gene databases

All output is linked to the NCBI or Ensembl databaes. Apart from output displayed in the web browser the user may download the result data.

 

We provide a computational validation of your calculation 

Using a recovery technique we estimate the performance of the ranking. This is also a measure of the quality of the seed. Ten percent of the seed is repedatly taken out and the position of this left out group in the rank is determind. A good performance results in a clear tendency to show high frequencies for top positions (left side). A random seed would result in a uniform distribution (flat histogram). An example of the output is given below. The raw data of the recovery test is also avialabe for download. In addition the user may obtain the figure of the individual recovery test in the jpeg, eps, or pdf format.

Example image of a recovery test

Results are (re-)accessible 

If you provide identical seed input, the system gives you fast access to your results that you have calculated previously. 

 

 
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