Literature Analysis

[Introduction] [Analysis procedure] [Output]

Introduction

The literature analysis page lists genes which are related with your gene of interest. For this purpose abstracts of more than 16 million scientific articles are scanned for more than 120,000 quality checked gene names, 455,000 synonyms as well as 350 function words from 8 vertebrates (human, mouse, rat, chicken, dog, zebra fish, cow, chimpanzee).

The first column of the table lists the synonym and description line for each of the genes cocited with your gene of interest.
The second column contains the GeneId of the gene 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 green.
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 (B0, B1, B2, B3) each show how many abstracts or sentences were found having citations for both genes on the respective level. Following the link will show a table view of the relevant sentences with the gene names and function words high-lighted.

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 cocited genes a button is available starting a complete BiblioSphere 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
B0	Abstract	Two genes are co-cited somewhere within an abstract	The transcription factors Wt1 and Eya1, the signaling molecules Gdnf and LIF and the receptors c-Ret and GdnfRalpha have been demonstrated to fulfil fundamental roles in the first step of metanephric induction , the outgrowth of the ureter.
B1	Sentence	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.
B2	Sentence & function word	Two genes are co-cited in a sentence which contains a function word like "regulates", "inhibits", "transactivates",...	WT1 and Pax2 are transcription factors involved in kidney development and phenotypic regulation of glomerular epithelial cells.
B3	Gene - function word - gene	Two genes are co-cited in one sentence and connected via a "function word".	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
Tissues
Function words