PIPs: Human Protein-Protein Interaction Prediction

Evidence of Interaction Between RFC4 and RFC3

The interaction score between RFC4 and RFC3 is 2.41E6.

This page provides the details about the evidence that was used to calculate the interaction Score between the two proteins

The Scores that are listed with each module are based on the interaction score where that module provides the only source of evidence. The final Score is the integration of all the sources of evidence.

Feature

Evidence

Score (?)

Gene Expression

Pearson's Correlation between RFC4 and RFC3 = 0.93

The original expression data was collated from the NCBI GEO database. For further information about this dataset please refer to the NCBI GEO dataset GDS596.

0.082

Orthology

Organism	RFC4 Orthologue		RFC3 Orthologue		Experiment
Organism	Accession	Inparalog Score	Accession	Inparalog Score	Experiment
bakers yeast	YJR068W	1	YBR087W	1	Y2H Immunoprecipitation Other SyntheticLethal AffinityCaptureMS AffinityCaptureWestern Get References From PubMed
worm	P53016	1	Q18547	1	Y2H Other Get References From PubMed
fly	Q9VX15	1	Q9U9Q1	1

The Inparalog Score is calculated by InParanoid

The experiment type Other refers to techniques other than Y2H, MS, Immunoprecipitation, SurfacePlasmonResonance, XrayDiffraction, Xlinking, CompetitionBinding, Immunofluorescence, GelRetardationAssay, AffinityChromatography, InVitroBinding, InVitro, InVivo, FarWestern, pullDown, AffinityCaptureMS, EpistaticMiniArrayProfile, AffinityCaptureWestern, BiochemicalActivity, CoCrystalStructure, FRET, ReconstitutedComplex, CoLocalization, CoPurification or CoFractionation.

3.01

Domains

Domains present in RFC4 and RFC3:

Domains in RFC4

Domains in RFC3

IPR003593	AAA ATPase
IPR003959	AAA ATPase, central region
IPR008921	DNA polymerase III clamp loader subunit, C-terminal
IPR000862	RFC
IPR013748	Replication factor C

IPR003593	AAA ATPase
IPR008921	DNA polymerase III clamp loader subunit, C-terminal
IPR000862	RFC

The Chi square scores for co-occurrence of domains that are present in RFC4 and RFC3 are listed below.

Domain 1		Domain 2		Chi Square
IPR008921	DNA polymerase III clamp loader subunit, C-terminal	IPR000862	RFC	1447.35
IPR000862	RFC	IPR000862	RFC	1295.13
IPR013748	Replication factor C	IPR000862	RFC	1125.48
IPR003959	AAA ATPase, central region	IPR000862	RFC	182.174
IPR003959	AAA ATPase, central region	IPR003593	AAA ATPase	133.351
IPR003593	AAA ATPase	IPR000862	RFC	128.851
IPR003593	AAA ATPase	IPR003593	AAA ATPase	89.0695

The background colour of the table refers to:

Blue Domain is only present in RFC4
Yellow Domain is only present in RFC3
Green Domain is present in both RFC4 and RFC3

0.265

Post-translational Modifications

No PTMs were used in calculating likelihood of interaction

Localisation

Protein: RFC4

Localisation	Reference
Nucleoplasm	HPRD

Protein: RFC3

Localisation	Reference
Nucleus	HPRD
Nucleolus	HPRD

Transitive Score

The common interactors between RFC4 and RFC3 that are considered by the Transitive module are listed below.

The Scores listed are the values used by the transitive module to calculate the final interaction Score between RFC4 andRFC3. The values listed are therefore not the final Score value for the listed interactions.

With a Score value ≥0.025 , RFC4 has 123 interactors and RFC3 has 110 interactors of which there are 90 common interactors.

Common Interactor	Name of Common Interactor	Score for RFC4-Interactor (?)	Score for RFC3-Interactor (?)
RFC5	RFC5: Replication factor C subunit 5	691.00	691.00
RFC2	RFC2: Replication factor C subunit 2	62.80	62.80
PCNA	PCNA: Proliferating cell nuclear antigen	54.70	54.70
RFC1	N/A	9.26	9.26
RAD17	RAD17, R24L: Cell cycle checkpoint protein RAD17	4.78	0.0258
MCM6	MCM6: DNA replication licensing factor MCM6	0.620	0.207
CHTF18	RUVBL, CHTF18: Protein CTF18 homolog.	0.354	0.354
ABCE1	ABCE1, RLI, OK/SW-cl.40, RNASEL1, RNASELI, RNS4I: ATP-binding cassette sub-famil	0.263	0.263
MCM4	MCM4, CDC21: DNA replication licensing factor MCM4	0.207	0.207
MCM5	MCM5, CDC46: DNA replication licensing factor MCM5	0.207	0.0968
CDC6	CDC6, CDC18L: Cell division control protein 6 homolog	0.207	0.207
MCM7	MCM7, CDC47, MCM2: DNA replication licensing factor MCM7	0.207	0.207
ORC6L	ORC6L: Origin recognition complex subunit 6	0.207	0.207
EIF2S1	EIF2S1, EIF2A: Eukaryotic translation initiation factor 2 subunit 1	0.207	0.0968
MCM2	MCM2, BM28, CCNL1, CDCL1, KIAA0030: DNA replication licensing factor MCM2	0.207	0.207
MCM3	MCM3: DNA replication licensing factor MCM3	0.207	0.207
KARS	KARS, KIAA0070: Lysyl-tRNA synthetase	0.137	0.137
TAF9	AK6, AD-004, CGI-137: Adenylate kinase isoenzyme 6	0.137	0.137
RUVBL1	RUVBL1, NMP238, TIP49, TIP49A: RuvB-like 1	0.123	0.074
TRIP13	TRIP13: Thyroid receptor-interacting protein 13	0.123	0.123
YBX1	YBX1, NSEP1, YB1: Nuclease sensitive element-binding protein 1	0.123	0.123
ATAD2	ATAD2, L16, PRO2000: ATPase family AAA domain-containing protein 2	0.123	0.123
SSBP1	SSBP1, SSBP: Single-stranded DNA-binding protein, mitochondrial precursor	0.117	0.263
DHX15	DHX15, DBP1, DDX15: Putative pre-mRNA-splicing factor ATP-dependent RNA helicase	0.108	0.108
POLR2H	POLR2H: DNA-directed RNA polymerases I, II, and III subunit RPABC3	0.0968	0.0968
YARS	YARS: Tyrosyl-tRNA synthetase, cytoplasmic	0.0968	0.123
ORC1L	ORC1L, ORC1, PARC1: Origin recognition complex subunit 1	0.0968	0.0968
RPA1	RPA1, REPA1, RPA70: Replication protein A 70 kDa DNA-binding subunit	0.0968	0.0968
BRCA2	BRCA2, FACD, FANCD1: Breast cancer type 2 susceptibility protein	0.083	0.083
KIAA0101	PAF, KIAA0101, L5, NS5ATP9: PCNA-associated factor	0.082	0.027
SMC4L1	N/A	0.082	0.027
PLK4	PLK4, SAK, STK18: Serine/threonine-protein kinase PLK4	0.081	0.081
PSMC1	PSMC1: 26S protease regulatory subunit 4	0.074	0.060
PSMC6	PSMC6, SUG2: 26S protease regulatory subunit S10B	0.074	0.060
ATAD3A	ATAD3A: ATPase family AAA domain-containing protein 3A	0.074	0.074
SCYE1	SCYE1, EMAP2: Multisynthetase complex auxiliary component p43 [Contains: Endothe	0.074	0.074
DARS	DARS, PIG40: Aspartyl-tRNA synthetase, cytoplasmic	0.074	0.074
PSMC3	PSMC3, TBP1: 26S protease regulatory subunit 6A	0.074	0.074
PSMC2	PSMC2, MSS1: 26S protease regulatory subunit 7	0.074	0.060
FXR1	FXR1: Fragile X mental retardation syndrome-related protein 1	0.074	0.060
SRP54	SRP54: Signal recognition particle 54 kDa protein	0.074	0.074
RUVBL2	RUVBL2, TIP48, CGI-46, TIP49B: RuvB-like 2	0.074	0.060
CKS2	CKS2: Cyclin-dependent kinases regulatory subunit 2	0.0739	0.0739
EIF5AP1	EIF5A: Eukaryotic translation initiation factor 5A-1	0.067	0.067
MDN1	MDN1, KIAA0301: Midasin	0.060	0.060
NARS	NARS, ASNS: Asparaginyl-tRNA synthetase, cytoplasmic	0.060	0.060
EIF1AX	EIF1AX, EIF1A, EIF4C: Eukaryotic translation initiation factor 1A, X-chromosomal	0.060	0.074
EXOSC2	EXOSC2, RRP4: Exosome complex exonuclease RRP4	0.060	0.060
EIF2B5	EIF2B5, EIF2BE: Translation initiation factor eIF-2B subunit epsilon	0.059	0.059
ORC2L	ORC2L, ORC2: Origin recognition complex subunit 2	0.059	0.059
ORC3L	ORC3L, LATHEO: Origin recognition complex subunit 3	0.053	0.039
CCNB2	CCNB2: G2/mitotic-specific cyclin-B2	0.051	0.051
CCNA2	CCNA2, CCN1, CCNA: Cyclin-A2	0.051	0.051
CCNB1	Cyclin B1	0.051	0.051
XRCC3	XRCC3: DNA-repair protein XRCC3	0.047	0.047
POLR2G	POLR2G: DNA-directed RNA polymerase II subunit RPB7	0.047	0.035
ASCC3	ASCC3, HELIC1: Activating signal cointegrator 1 complex subunit 3	0.047	0.047
BCS1L	BCS1L, BCS1: Mitochondrial chaperone BCS1	0.044	0.044
GCLC	GCLC, GLCL, GLCLC: Glutamate--cysteine ligase catalytic subunit	0.044	0.044
EIF1AY	EIF1AY: Eukaryotic translation initiation factor 1A, Y-chromosomal	0.044	0.044
VCP	VCP: Transitional endoplasmic reticulum ATPase	0.044	0.044
BARD1	BARD1: BRCA1-associated RING domain protein 1	0.042	0.042
SRPR	SRPR: Uncharacterized protein SRPR	0.041	0.041
NUBP1	NUBP1, NBP, NBP1: Nucleotide-binding protein 1	0.036	0.044
PEX1	PEX1: Peroxisome biogenesis factor 1	0.036	0.028
VPS4A	VPS4A, VPS4: Vacuolar protein sorting-associating protein 4A	0.036	0.036
XAB1	XAB1, MBDIN, HUSSY-23: XPA-binding protein 1	0.0331	0.074
RFC1	RFC1, RFC140: Replication factor C subunit 1	0.0288	0.0288
VPS4B	VPS4B, SKD1, VPS42: Vacuolar protein sorting-associating protein 4B	0.028	0.028
C18orf56	N/A	0.027	0.027
ITGB3BP	N/A	0.027	0.027
CDCA8	CDCA8, PESCRG3: Borealin	0.027	0.027
TPX2	TPX2, C20orf1, C20orf2, DIL2, HCA519: Targeting protein for Xklp2	0.027	0.027
NOLC1	NOLC1, KIAA0035: Nucleolar phosphoprotein p130	0.027	0.027
CKAP2	CKAP2, LB1, TMAP: Cytoskeleton-associated protein 2	0.027	0.027
HMMR	HMMR: Hyaluronan-mediated motility receptor	0.027	0.027
MCM10	N/A	0.027	0.027
C22orf18	N/A	0.027	0.027
TMPO	N/A	0.027	0.027
RAD51AP1	N/A	0.027	0.027
ZWINT	N/A	0.027	0.027
GMNN	GMNN: Geminin	0.027	0.027
CLPX	CLPX: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial pr	0.027	0.060
AFG3L2	AFG3L2: AFG3-like protein 2	0.027	0.060
PRSS15	LONP1, PRSS15: Lon protease homolog, mitochondrial precursor	0.027	0.060
DNAH11	N/A	0.027	0.027
RAD51L3	RAD51L3, RAD51D: DNA repair protein RAD51 homolog 4	0.027	0.027
RPA3	RPA3, REPA3, RPA14: Replication protein A 14 kDa subunit	0.027	0.027
RAD51L1	RAD51L1, RAD51B, REC2: DNA repair protein RAD51 homolog 2	0.027	0.027
CCNF	CCNF: G2/mitotic-specific cyclin-F	0.027	0.027

0.572

Total Score

2.41E6