In this work, an GO4Cancer for revealing function changes from rewiring regulations by network ontology analysis was proposed.
- GO4Cancer: A GO4Cancer fremework is proposed to evaluate the results of rewiring networks which is more similar to phenotype.
- If you have any questions about GO4Cancer, please directly contact the corresponding author Prof. Zhi-Ping Liu with the E-mail: zpliu@sdu.edu.cn
Chang, Yaohua, et al. "XXX." Submit to XXX.
- R file gives all R codes used in this work.
- Data file gives some necessary input/output files by the R codes.
- Here are two examples. Other cancer data can be downloaded from the website.
- Some of these input files only give the first few lines, but this does not affect the results of the work (GO4Cancer).
- In the Supplementary file file, we present the necessary Additional files contained in our work.
The serial number (1), (2), ..., (14) represents the order in which the program runs in our work.
- (1) donut picture.R -- The number of genes in 17 cancers in KEGG and MalaCards databases is graphically presented.
- (2) GFEA.R -- Gene functional enrichment analysis. The function of 17 cancers is enriched in this way.
- (3) enrich go seventheen.R -- The number of functions in 17 cancers in KEGG and MalaCards databases is graphically presented.
- (4) Enriched and Deredun.R -- Enrichment of cancer functions and deredundancy.
- (5) deredun.R -- De-redundancy process. Retain more specific GO terms.
- (6) dot plot_Redun.R -- dot diagram after removing redundancy.
- (7) spe GO 17.R -- Specific GO terms for 17 cancers are presented.
- (8) SPE_CON.R -- Specificity and Consistency in 17 cancers.
- (9) Gen_network.R -- Establish Gene Co-expression Network.
- (10) terms similarity.R -- Calculate the semantic similarity between GO terms.
- (11) iNOA.R -- An Improvement of Network Ontology Analysis with GO Semantic Similarity.
- (12) NetGOterms.R -- The process of network functions.
- (13) CN_NO_net _compa.R -- Comparison of disease and normal network and phenotype in endometrial cancer.
- (14) Rand 30t.R -- Take 30 GO terms randomly from all the GO terms and take the mean value.
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