BioMed Research International / 2016 / Article / Tab 1

Research Article

PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data

Table 1

Interaction databases used to create a PPI netpwork. Databases marked with an asterix () had been taken from the IMEx interface (http://www.ebi.ac.uk/intact/imex/main.xhtml) instead from direct database sources. An interaction was counted as invalid with one of the following reasons: it does not have a valid UniProt accession number or it could not be mapped to one, it has no valid gene name or it could not be mapped to one, or it has no valid taxonomy ID or it could not be mapped to one. Unfortunately, some mapping processes do not yet cover a large percentage of specific databases (cf. DIP with 97% invalid interactions or InnateDB with 100% invalid interactions).

NameDateInteractionsIMEx
TotalInvalidValid

Mentha17.08.14461,40847.236 (10%)414.172 (90%)
IntAct18.07.14424,706128.680 (28%)326.026 (72%)
BioGRID01.08.14749,913493.819 (66%)256.094 (34%)
MINT26.03.13122,35617.968 (15%)104.388 (85%)
PIPs12.09.0834,2169.466 (28%)24.750 (72%)
HPRD13.04.1039,24029.288 (75%)9.952 (25%)
UniProt18.08.1411,9192.272 (19%)9647 (81%)
DIP07.01.14107,619104.050 (97%)3.569 (03%)
MPIDB18.08.141,759767 (44%)992 (56%)
I2D18.08.141,117263 (24%)854 (76%)
BHF-UCL18.08.14911315 (35%)596 (65%)
InnateDB17.08.1468093 (14%)587 (86%)
MatrixDB18.08.141,244864 (69%)380 (31%)
MolCon18.08.14495129 (26%)366 (74%)
MBInfo18.08.14638306 (48%)332 (52%)

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