Genom 2005 is a feature rich and user friendly application for analysing array-experiments (e.g. from provider Affymetrix).
Many publications have been released about our previous developed program gEn0M (GENOM 2005 is the successor of gEn0M). Please take a look at the publications page for some of them.

Features for microarray analysis software

• Analysis of AffyMetrix-Arrays (cDNA-Arrays or similar technologies could be easily integrated as well)
• Normalisation of raw data
• Many additional gene information (official gene names, location, function prediction, sequences, database references (GeneOntology, InterPro, SwissPROT, ENSEMBL, GeneBank...)
• Multiple analysis methods (cluster, Support-Vector-Machine, statistical methods (e.g. TTest))
• Automatic pathway mapping (BioCarta, GenMAPP, KEGG...)
• Integrated pathway editor (user friendly drag and drop operation)
• Function prediction
• Sequence analysis

Genom 2005 presents the data in different colours for each signal, so you have a quick overview of the data. Also a gene name and an accession number for each probeset is presented concurrently.

This is a diagram with one array. It shows a bar for each probeset.

You can display each signal on your array in a 3D view. When comparing it with another array you can easily find interesting probesets. You can also sort the signals by gene function or gene location.

This view displays all probesets orders by their location on the chromosome.

This screenshot shows a graph where every probeset is represented by a line. It shows the up/down regulation of a gene between different time.

This screenshot shows a loaded pathway which is directly combined with the array data you have loaded.

With this integrated map editor, you can easily create new pathways or edit existing one.

Often you have no information about a probeset because it's an EST or it has not been analysed before. With this module you can get new information from probesets or custom sequences over a BLAST search (online). Possible new gene functions will then be shown.

Details about the function prediction.

PubMED is the largest database in the world with medical articles (hosted on Ncbi website). This module searches that database and returns relevant results to the entered term (or gene).

MeSH (Medical Subject Headings) provides ordered terms to improve PubMED searches for example.

The relationship of the genes described in the abstracts from PubMED are shown here as relationship diagram.

This algorithm presents the data in a table with all the gene functions from the genes you previously filtered, or can be done for the whole array.

This displays the gene functions in a GeneOntology like view.

The gene information dialog. Here you get more detail information from the searched query like sequence, description and more.

In this screenshot, you can directly access the links for more information about your query. Unlike in other programs you can click on a link and directly access the result page without filling out web forms.

Another GeneOntology graph of the gene functions from the gene.

In this screenshot you can see direct links for more information about your query. Unlike in other programs you can click on a link and get directly to the result page without filling out web forms.

This cluster can be made easily. It shows the most equal values paired together in a graph.

Another view from the cluster algorithm.

All arrays from Affymetrix are supported. New systems can easily be implemtened on request.

Supported affymetrix arrays

                 AG     ATH1-121501         Barley1
          Bsubtilis          Canine         Chicken
           Celegans     DrosGenome1    Drosophila_2
         Ecoli_ASv2           Ecoli        E_coli_2
            HC_g110        HG-Focus      HG-U133A_2
           HG-U133A        HG-U133B  HG-U133_Plus_2
          HG_U95Av2          HuEx-1         HG_U95B
            HG_U95C         HG_U95D         HG_U95E
             Hu6800           Maize        Medicago
          HG_U74Av2       MG_U74Bv2       MG_U74Cv2
            MOE430A         MOE430B     Mouse430A_2
         Mouse430_2       Mu11KsubA       Mu11KsubB
      Nimble-Arrays        Porchine         RAE230A
            RAE230B        Rat230_2         RG_U34A
            RG_U34B         RG_U34C            Rice
             RN_U34          RT_U34         Pae_G1a
Pasmodium_Anopheles      Sugar_Cane         Soybean
           S_aureus          Tomato        U133_X3P
     Vitis_Vinifera  Xenopus_laevis         Yeast_2
             YG_S98       Zebrafish          Bovine
          Hu35KsubB       Hu35KsubC       Hu35KsubD
          Hu35KsubA    HuGeneFlsubA    HuGeneFlsubB
       HuGeneFlsubC    HuGeneFlsubD  HuGeneFl Array
            MG-U74A         MG-U74B         MG-U74C
          Mu19KsubA       Mu19KsubB       Mu19KsubC
         Mu6500subA      Mu6500subB      Mu6500subC
         Mu6500subD           Wheat            ....