GOpredict

A data frame returned from the function "SignificantPairs"

Pfile

A 2-column data frame consisting of binary interactions where each row i.e. c(A, B) represents an undirected edge (interaction) between gene A and gene B.

PPIdb

A list that maps GO ID to genes. The names should be gene symbols and the elements should be GO IDs. i.e. $SHC1 [1] "GO:0005158" "GO:0005068" "GO:0005159" "GO:0070435" $POU5F1 [1] "GO:0035413" "GO:0003130" "GO:0060391" "GO:0090308" "GO:0060965" "GO:0035198" $FGF12 [1] "GO:0008201" ......

Gene2Annotation

A cut-off for p-values from Fishers exact test when predicting GO annotations

p_value


This function uses a direct annotation scheme to predict GO annotations for proteins in the network derived with the PAND algorithm


PANDA (Preferential Attachment based common Neighbor Distribution derived Associations) is designed to perform the following tasks in PPI networks: (1) identify significantly functionally associated protein pairs, (2) predict GO terms and KEGG pathways for proteins, (3) make a cluster of proteins based on the significant protein pairs, (4) identify subclusters whose members are enriched in KEGG pathways. For other types of biological networks, (1) and (3) can still be performed.

Hua Li

PANDA

Preferential Attachment Based Common Neighbor Distribution
Derived Functional Associations

GOpredict function

A list that maps GO ID to genes. The names should be gene symbols and the elements should be GO IDs. i.e.

    $SHC1

    [1] "GO:0005158" "GO:0005068" "GO:0005159" "GO:0070435"

    $POU5F1

    [1] "GO:0035413" "GO:0003130" "GO:0060391" "GO:0090308" "GO:0060965" "GO:0035198"

    $FGF12

    [1] "GO:0008201"

    ......

GOpredict: Predict GO annotations for proteins

Description

Usage

Arguments

Value

See Also