RNAiCut: Automated Detection of Significant Genes from Functional Genomic Screens

Input Genes
(if doing local scrambling, input genes and their corresponding scores, with the genes and scores separated by tabs):


CG Names
FBGN Identifiers
Official Gene Names
Non-Fly Names (for worm, human, or possibly your own network)



Do Local Scrambling:

Local Scrambling Range:
(0.00-4.00 or higher, leave blank for no local scrambling)








User Guide

Links to and Citations for Networks

Enrichment Results Tables

Network to Query (Compiled Knowledge Sources): Description:
D. melanogaster PPI Network This is a network of experimentally-determined protein interactions in fly. This network contains more genes than cell localization but fewer genes than gene expression. Because the data in this network comes from only 1 species, the threshold it provides may miss some significant genes.
D. melanogaster PPI with PPI Mapped from Other Species Network This network was created through a multiple alignment of the PPI networks of fly, worm, and human with the Isorank program. This network contains more genes than cell localization but fewer genes than gene expression.
C. elegans PPI Network This network is also based on experimental data. Submit C. elegans gene names.
H. sapiens PPI Network This network is also based on experimental data. Submit human gene names.
D. melanogaster Co-Expression Network An edge in this network indicates that the corresponding genes are co-expressed, as inferred from the NCBI GEO gene expression database. This network has more genes than the other networks. In addition, because it is very cliquish, the threshold is later than for the other networks and therefore may provide extraneous genes.
D. melanogaster Cellular Co-Localization Network An edge in this network indicates that the corresponding genes are localized to the same cellular compartment(s). This network is the newest network. It therefore contains fewer genes than the other networks and may be less reliable.
Upload Your Own Network

Upload your own biological network below. This network should be a text file. Each line in the text file should have two genes that are connected in your network. The genes should be separated with a tab. Make sure to choose the appropriate gene names.

Please cite Kaplow, I. M., Singh, R., Friedman, A., Bakal, C., Perrimon, N., and Berger, B. RNAiCut: Automated Detection of Significant Genes from Functional Genomic Screens.

Please also cite the sources of the networks you used. See "Links to and Citations for Networks" link for network citations. If you are using the enrichment results table, please include the citations at the bottom of the "Enrichment Results Tables" link.

Site is based on Funspec from Grigull et al.