Literature Analysis

Introduction

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.

The first column of the table lists the symbol and name for each of the genes co-cited with your gene of interest.
The second column contains the Gene ID linked to the respective information at the NCBI.
The third column denotes if the co-cited gene is a known transcription factor. For transcription factors the associated matrix from the Genomatix Matrix Library is listed. Transcription factors that in addition have a binding site in a promoter of the gene of interest are highlighted in blue.
If there is no matrix description available for a transcription factor so far, this is indicated by the term no matrix.
The columns for the four different citation levels (see below) each show how many abstracts or sentences were found having citations for both genes on the respective level. Clicking the link will show a table view of the relevant sentences with the gene names high-lighted (output format as in LitInspector).

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:

Transcription factor genes
Non-transcription factor genes
Function words