Statistics iRefIndex 2.0

Assignment of protein interactors to ROG's

Source	Intractors	Assigned	%	Arbitrary	New	Unassigned	Unique proteins
bind	285482	273695	95.87	0	7782	4005	40766
grid	28218	19295	68.38	8843	3	77	26945
intact	89190	85695	96.08	19	3250	226	39678
mint	80543	77294	95.97	6	2764	479	28055
MPPI	3628	3281	90.44	178	33	136	857
ophid	146423	145408	99.31	103	653	259	9663
All	633484	604668	95.45	9149	14485	5182	77745

Summary of mapping interaction records to RIG's.

Source	Total records	Protein-only interactors	PPI Assigned to RIGID	Unique RIGIDs
bind	193648	93957	91234(97.1019%)	62859(68.8987%)
grid	218165	218165	217902(99.8794%)	142872(65.5671%)
intact	111572	111008	110598(99.6307%)	97012(87.7159%)
mint	104847	104847	103522(98.7363%)	73733(71.2245%)
HPRD	38037	38037	38017(99.9474%)	37980(99.9027%)
ophid	73257	73257	72907(99.5222%)	47318(64.9019%)
MPACT	16504	16504	16286(98.6791%)	13321(81.7942%)
MPPI	1814	1814	1695(93.4399%)	827(48.7906%)
ALL	757844	657589	652161(99.1746%)	475922(72.9762%)

Features of the ROG assignment score and their corresponding character representation

Character	Description of feature (when the value is 1)	Frequency
D	The source database (D) listed in the interaction record is different than what is expected for the given accession for the protein. In specific cases, this difference is tolerated and the assignment is made.	12719(2.0243%)
E	The protein reference was a retired NCBI Identifier. NCBI\'s eUtils (E) were used to retrieve the current accession and/or sequence.	10909(1.7363%)
G	The interaction record\'s reference for the protein was an EntrezGene (G) identifier. The corresponding products of the gene were used to make the assignment.	0(0.0%)
L	More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods)	9150(1.4563%)
M	The protein reference listed by the interaction record was a typographical modification (M) of a known accession. In specific cases, this variation is tolerated and the assignment is made.	1882(0.2995%)
+	More than one possible assignment is possible (+). This case may arise in one of three ways. 1) The reference supplied by the interaction record requires updating but more than one possibility exists. For example, Q7XJL8 was found to be a secondary accession in three separate UniProt records (Q3EBZ2, Q6DR20, and Q8GWA9). 2) The secondary references supplied by the interaction record point to more than one unique protein sequence. 3) An EntrezGene identifier is provided in the interaction record as a protein reference. This identifier points to more than one protein product. An attempt is made to resolve this ambiguity as indicated by ROG score features O, X or L (see below).	9172(1.4598%)
N	The protein reference, taxonomy identifier and sequence for the protein as provided in the interaction record are used to make a new entry in the SEGUID table. The protein interactor is assigned the newly (N) generated ROG identifier.	14485(2.3054%)
O	More than one possible assignment is possible (see + above). The assignment chosen has a SEGUID that is identical to the SEGUID of the original (O) sequence provided in the interaction record.	22(0.0035%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	13495(2.1479%)
U	The protein reference listed in the interaction record and used to make the assignment was a secondary UniProt accession and was updated (U) to a primary UniProt accession in order to make the assignment.	20644(3.2857%)
T	The taxonomy (T) identifier for the protein (as supplied by the interaction record) differed from what was found in the protein sequence record. This discrepancy was tolerated and the assignment was made	24056(3.8287%)
V	The protein reference listed by the interaction record contained version (V) information that was ignored. For example, RefSeq accession.version NP_012420.1 was listed but treated as RefSeq accession NP_012420.	0(0.0%)
Q	The protein reference used to make the assignment was of the type \'see-also\'. See PSI-MI Path: entrySet/entry/interactorList/interactor/xref/primaryRef/refType = \'see-also\'.	27(0.0043%)
P	The interaction record\'s primary (P) reference for the protein was used to make the assignment	584548(93.0362%)
S	One of the interaction record\'s secondary (S) references for the protein was used to make the assignment	43754(6.9638%)
X	More than one possible assignment is possible (see + above). The assignment chosen has the same taxonomy (X) identifier as listed in the interaction record	35(0.0056%)

Number of protein references successfully assigned to ROG's and broken down by assignment score

Binary_flag	String_score	Score_class	Proteins	Percentage	BIND	BioGrid	DIP	MINT	HPRD	OPHID	MIIP	MPACT
010101000100000010	SLEN+	-1	1	0.0002%	0	1	0	0	0	0	0	0
010100000000010001	PTEN	-1	18	0.0028%	0	0	0	0	0	0	18	0
010000000010010001	PTMN	-1	2	0.0003%	0	0	0	0	0	0	2	0
000001010100000010	SXL+	-1	1	0.0002%	0	0	0	0	0	0	0	0
100000000000000101	PUQ	-1	1	0.0002%	0	0	0	0	0	0	0	0
000000000010010010	STM	-1	3	0.0005%	0	3	0	0	0	0	0	0
000000001100010101	PUTO+	-1	15	0.0024%	0	0	0	0	0	0	0	0
000000000000000001	P	1	523340	82.6130%	232755	7313	0	74939	0	126446	0	0
000010000000000001	PI	1	19	0.0030%	0	2	0	0	0	0	0	0
000010000001000010	SDI	1	1066	0.1683%	1044	22	0	0	0	0	0	0
000010000001000001	PDI	1	40	0.0063%	0	0	0	0	0	0	0	0
000010000000000010	SI	1	11457	1.8086%	11287	170	0	0	0	0	0	0
000000000010000010	SM	1	1190	0.1879%	0	1190	0	0	0	0	0	0
000000000001000010	SD	1	6	0.0009%	0	6	0	0	0	0	0	0
000000000000000010	S	1	8209	1.2958%	0	7754	0	236	0	0	0	0
000000000001000001	PD	1	9244	1.4592%	8091	1134	0	19	0	0	0	0
000000000010000001	PM	1	488	0.0770%	473	1	0	0	0	0	0	0
000000000000000101	PU	2	19850	3.1335%	0	0	0	346	0	18835	0	0
000000000000000110	SU	2	286	0.0451%	0	275	0	5	0	0	0	0
000100000000000001	PE	2	246	0.0388%	0	0	0	0	0	0	0	0
000000001100000110	SUO+	2	1	0.0002%	0	0	0	0	0	0	0	0
000000001100000101	PUO+	2	6	0.0009%	0	0	0	1	0	0	0	0
000100000000000010	SE	2	5434	0.8578%	5434	0	0	0	0	0	0	0
000010000001010010	STDI	3	66	0.0104%	29	37	0	0	0	0	0	0
000010000000010010	STI	3	834	0.1317%	826	8	0	0	0	0	0	0
000010000001010001	PTDI	3	13	0.0021%	0	0	0	0	0	0	0	0
000000000001010001	PTD	3	1483	0.2341%	1483	0	0	0	0	0	0	0
000000000000010010	ST	3	1383	0.2183%	0	1380	0	0	0	0	0	0
000000000000010001	PT	3	19265	3.0411%	11825	0	0	1742	0	122	3072	0
000000000010010001	PTM	3	199	0.0314%	132	0	0	0	0	0	67	0
000100000000010010	STE	4	316	0.0499%	316	0	0	0	0	0	0	0
000100000000010001	PTE	4	2	0.0003%	0	0	0	0	0	0	0	0
000001000100000101	PUL+	5	84	0.0133%	0	0	0	0	0	84	0	0
000001000100010101	PUTL+	5	187	0.0295%	0	0	0	1	0	0	178	0
000001000100000010	SL+	5	8843	1.3959%	0	8843	0	0	0	0	0	0
100000000000000001	PQ	5	2	0.0003%	0	0	0	0	0	0	0	0
000001010100000101	PUXL+	5	34	0.0054%	0	0	0	5	0	19	0	0
000000000000010101	PUT	5	180	0.0284%	0	0	0	6	0	5	142	0
100000000000010001	PTQ	5	24	0.0038%	0	0	0	0	0	0	0	0
010100000000010010	STEN	6	22	0.0035%	22	0	0	0	0	0	0	0
010100000000000010	SEN	6	4636	0.7318%	4635	0	0	1	0	0	0	0
010100000000000001	PEN	6	234	0.0369%	0	0	0	0	0	0	0	0
010000000001000001	PDN	6	801	0.1264%	799	2	0	0	0	0	0	0
010000000000000001	PN	6	8727	1.3776%	2322	0	0	2763	0	653	11	0
010000000000010001	PTN	6	44	0.0069%	4	0	0	0	0	0	2	0

Redundancy between pairs of interaction datasets processed in this study

BIND	40766	'	'	'	'	'	'	'	'
BIOGRID	14613	26945
DIP	0	0	0
HPRD	0	0	0	0
INTACT	18047	16580	0	0	39678
MINT	16465	15288	0	0	22659	28055
MPACT	0	0	0	0	0	0	0
MPPI	647	181	0	0	548	539	0	857
OPHID	3172	2732	0	0	5549	4796	0	404	9663
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID
	20177	0	2301	3476	8162	0	0	53	12338