Overview of Help-Pages

Literature Analysis


The literature analysis page lists genes which are related with your gene of interest. For this purpose abstracts of more than 21 million scientific articles from PubMed are scanned for more than 900.000 quality checked gene names and synonyms from human and several animal and plant species.

Each of the columns can be sorted using the respective link in the header of the table.

For the gene of interest and each of the co-cited genes a button is available starting a complete Genomatix Pathway System (GePS) analysis of the respective gene.

Literature Analysis

To cover the range from "possibly related" - to "most likely related" genes, Genomatix calculates different levels of gene-gene co-citations. The following table explains the co-citation levels and shows an output example:

Level Description Example
Abstract level Two genes are co-cited somewhere within an abstract

An expression of Wt1 gene was tested additionally. An analysis of ABL control gene was used to normalize of achieved results.

Sentence level Two genes are co-cited within the same sentence

These transcription factors include Pax2, WT1 (the Wilms tumor suppressor gene), Pod1 (capsulin, epicardin), Kreisler (maf-1), lmx1b, and mf2.

Function Word Two genes are co-cited in a sentence which contains a function word like "regulation", "inhibits", "transactivates",...

WT1 and Pax2 are transcription factors involved in kidney development and phenotypic regulation of glomerular epithelial cells.

Genomatix Expert Two genes are co-cited in one sentence and the significance of the gene to gene relation was validated by a scientific expert.

PAX2 transactivated the WT1 promoter up to 35-fold in CHO-K1 cells, and from four- to sevenfold in 293 cells.

As can be seen from the examples above, the gene names/synonyms, tissues and function words are highlighted in the sentences by the different colors: