(77 nodes) Base Excision Repair network (Manihot esculenta)

Nodes:

Network nodes represent proteins

splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.

Node Color

colored nodes:
query proteins and first shell of interactors

white nodes:
second shell of interactors

Node Content

empty nodes:
proteins of unknown 3D structure

filled nodes:
a 3D structure is known or predicted

Edges:

Edges represent protein-protein associations

associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.

Known Interactions

from curated databases

experimentally determined

Predicted Interactions

gene neighborhood

gene fusions

gene co-occurrence

Others

textmining

co-expression

protein homology

Your Input:
	A0A2C9V9P1	Macro domain-containing protein. (745 aa)
	A0A2C9WEG8	ATPase_AAA_core domain-containing protein. (1256 aa)
	A0A2C9WEK2	AAA domain-containing protein. (342 aa)
	A0A2C9WLH4	Proliferating cell nuclear antigen; This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand; Belongs to the PCNA family. (266 aa)
	A0A2C9WN70	Uncharacterized protein. (789 aa)
	A0A2C9WNH3	Poly [ADP-ribose] polymerase. (633 aa)
	A0A2C9WNK7	NAC domain-containing protein. (516 aa)
	A0A2C9WP85	Uncharacterized protein. (617 aa)
	A0A2C9WPW4	NAC domain-containing protein. (513 aa)
	A0A2C9WQF6	Poly [ADP-ribose] polymerase. (621 aa)
	A0A2C9WR64	NAC domain-containing protein. (68 aa)
	A0A2C9VPX4	AAA domain-containing protein. (1034 aa)
	A0A2C9VR50	CMP/dCMP-type deaminase domain-containing protein. (1373 aa)
	A0A2C9VS54	Uncharacterized protein. (238 aa)
	A0A2C9VU82	NAC domain-containing protein. (494 aa)
	A0A2C9VVE7	CMP/dCMP-type deaminase domain-containing protein. (435 aa)
	A0A2C9VVY5	Poly [ADP-ribose] polymerase. (984 aa)
	A0A2C9VY61	Uncharacterized protein. (541 aa)
	A0A2C9VYJ6	DNA polymerase epsilon catalytic subunit; DNA polymerase II participates in chromosomal DNA replication; Belongs to the DNA polymerase type-B family. (2223 aa)
	NTH1	Endonuclease III homolog; Bifunctional DNA N-glycosylase with associated apurinic/apyrimidinic (AP) lyase function that catalyzes the first step in base excision repair (BER), the primary repair pathway for the repair of oxidative DNA damage. The DNA N-glycosylase activity releases the damaged DNA base from DNA by cleaving the N-glycosidic bond, leaving an AP site. The AP lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination. Primarily recognizes and repairs oxidative base damage of pyrimidines. (362 aa)
	A0A2C9VZY1	Replication factor C subunit 1. (984 aa)
	A0A2C9VZZ5	Histone H2B; Belongs to the histone H2B family. (143 aa)
	A0A2C9W0H3	Histone H2B; Belongs to the histone H2B family. (147 aa)
	A0A2C9W1T8	BRCT domain-containing protein. (380 aa)
	A0A2C9W5P7	Uracil-DNA glycosylase; Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. (312 aa)
	A0A2C9W6U2	Replication protein A subunit; Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication. The activity of RPA is mediated by single-stranded DNA binding and protein interactions. Probably involved in repair of double-strand DNA breaks (DSBs) induced by genotoxic stresses. (668 aa)
	A0A2C9WAM4	AAA domain-containing protein. (335 aa)
	A0A2C9WBK4	CMP/dCMP-type deaminase domain-containing protein. (153 aa)
	A0A2C9WD70	Proliferating cell nuclear antigen; This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand; Belongs to the PCNA family. (264 aa)
	A0A2C9VP72	Replication protein A subunit; Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication. The activity of RPA is mediated by single-stranded DNA binding and protein interactions. Probably involved in repair of double-strand DNA breaks (DSBs) induced by genotoxic stresses. (624 aa)
	A0A2C9VFW2	CMP/dCMP-type deaminase domain-containing protein. (186 aa)
	A0A2C9VHU3	AAA domain-containing protein. (354 aa)
	A0A2C9VJU8	Histone H2B; Belongs to the histone H2B family. (140 aa)
	A0A2C9U3P5	CCHC-type domain-containing protein. (163 aa)
	A0A2C9U3H1	Uncharacterized protein. (397 aa)
	A0A2C9U352	Uncharacterized protein. (395 aa)
	A0A2C9U2G1	Rep_fac_C domain-containing protein. (252 aa)
	A0A251LJ82	ENDO3c domain-containing protein. (412 aa)
	A0A251KRR0	NAC domain-containing protein. (373 aa)
	FEN1-2	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...] (415 aa)
	FEN1	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...] (383 aa)
	A0A251JWR0	DNA ligase. (804 aa)
	MANES_S022500	Histone H2B; Belongs to the histone H2B family. (139 aa)
	MANES_S091500	Uncharacterized protein. (226 aa)
	A0A0M5JKF0	NAC transcription factors 92. (383 aa)
	A0A0M4G3S7	NAC transcription factors 94. (292 aa)
	A0A0M3R849	NAC transcription factors 3. (581 aa)
	A0A2C9VNN1	Uncharacterized protein. (354 aa)
	A0A2C9VM95	Histone H2B; Belongs to the histone H2B family. (139 aa)
	A0A2C9VLX3	Uncharacterized protein. (478 aa)
	A0A2C9VLV1	AAA domain-containing protein. (1262 aa)
	A0A2C9VA78	NAC domain-containing protein. (245 aa)
	A0A2C9VAA3	NAC domain-containing protein. (185 aa)
	A0A2C9VB35	CMP/dCMP-type deaminase domain-containing protein. (186 aa)
	A0A2C9VBM3	Uncharacterized protein. (127 aa)
	A0A2C9VDC3	Uncharacterized protein. (268 aa)
	A0A2C9VDY7	NAC domain-containing protein. (254 aa)
	A0A2C9VEK0	Uncharacterized protein. (429 aa)
	A0A2C9U592	Replication protein A subunit; Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication. The activity of RPA is mediated by single-stranded DNA binding and protein interactions. Probably involved in repair of double-strand DNA breaks (DSBs) induced by genotoxic stresses. (849 aa)
	A0A2C9U5A0	AAA domain-containing protein. (1195 aa)
	A0A2C9U9R7	AAA domain-containing protein. (1193 aa)
	A0A2C9UFJ3	PARP-type domain-containing protein. (397 aa)
	A0A2C9UJB5	Uncharacterized protein. (591 aa)
	A0A2C9UMR5	AAA domain-containing protein. (1284 aa)
	A0A2C9UNR1	NAC domain-containing protein. (623 aa)
	A0A2C9UP90	Uncharacterized protein. (263 aa)
	A0A2C9UPD1	Adenine DNA glycosylase; Adenine glycosylase active on G-A mispairs. (465 aa)
	A0A2C9US28	CMP/dCMP-type deaminase domain-containing protein. (591 aa)
	A0A2C9USN2	Uncharacterized protein. (264 aa)
	A0A2C9V0M4	BRCT domain-containing protein. (252 aa)
	A0A2C9V112	Histone H2B; Belongs to the histone H2B family. (147 aa)
	A0A2C9V1K4	Histone H2B; Belongs to the histone H2B family. (145 aa)
	A0A2C9V1K5	Histone domain-containing protein; Belongs to the histone H2B family. (233 aa)
	A0A2C9V1W9	CBFD_NFYB_HMF domain-containing protein. (161 aa)
	A0A2C9V2Z2	Poly [ADP-ribose] polymerase. (824 aa)
	A0A2C9V3L1	Histone H2B; Belongs to the histone H2B family. (139 aa)
	A0A2C9V8D2	Uncharacterized protein. (650 aa)

Your Current Organism:

Manihot esculenta

NCBI taxonomy Id: 3983
Other names: M. esculenta, Manihot esculenta Crantz, Manihot utilissima, cassava, manioc, tapioca, yuca

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

a tab-delimited file containing all known functional terms of proteins in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
A0A0M3R849	A0A251JWR0	A0A0M3R849	A0A251JWR0	NAC transcription factors 3.	DNA ligase.	0.420
A0A0M3R849	A0A2C9U2G1	A0A0M3R849	A0A2C9U2G1	NAC transcription factors 3.	Rep_fac_C domain-containing protein.	0.552
A0A0M3R849	A0A2C9U5A0	A0A0M3R849	A0A2C9U5A0	NAC transcription factors 3.	AAA domain-containing protein.	0.414
A0A0M3R849	A0A2C9U9R7	A0A0M3R849	A0A2C9U9R7	NAC transcription factors 3.	AAA domain-containing protein.	0.414
A0A0M3R849	A0A2C9UMR5	A0A0M3R849	A0A2C9UMR5	NAC transcription factors 3.	AAA domain-containing protein.	0.414
A0A0M3R849	A0A2C9V1W9	A0A0M3R849	A0A2C9V1W9	NAC transcription factors 3.	CBFD_NFYB_HMF domain-containing protein.	0.400
A0A0M3R849	A0A2C9V8D2	A0A0M3R849	A0A2C9V8D2	NAC transcription factors 3.	Uncharacterized protein.	0.469
A0A0M3R849	A0A2C9VEK0	A0A0M3R849	A0A2C9VEK0	NAC transcription factors 3.	Uncharacterized protein.	0.414
A0A0M3R849	A0A2C9VHU3	A0A0M3R849	A0A2C9VHU3	NAC transcription factors 3.	AAA domain-containing protein.	0.469
A0A0M3R849	A0A2C9VLV1	A0A0M3R849	A0A2C9VLV1	NAC transcription factors 3.	AAA domain-containing protein.	0.414
A0A0M3R849	A0A2C9VPX4	A0A0M3R849	A0A2C9VPX4	NAC transcription factors 3.	AAA domain-containing protein.	0.414
A0A0M3R849	A0A2C9VYJ6	A0A0M3R849	A0A2C9VYJ6	NAC transcription factors 3.	DNA polymerase epsilon catalytic subunit; DNA polymerase II participates in chromosomal DNA replication; Belongs to the DNA polymerase type-B family.	0.573
A0A0M3R849	A0A2C9VZY1	A0A0M3R849	A0A2C9VZY1	NAC transcription factors 3.	Replication factor C subunit 1.	0.615
A0A0M3R849	A0A2C9WAM4	A0A0M3R849	A0A2C9WAM4	NAC transcription factors 3.	AAA domain-containing protein.	0.579
A0A0M3R849	A0A2C9WD70	A0A0M3R849	A0A2C9WD70	NAC transcription factors 3.	Proliferating cell nuclear antigen; This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand; Belongs to the PCNA family.	0.714
A0A0M3R849	A0A2C9WEG8	A0A0M3R849	A0A2C9WEG8	NAC transcription factors 3.	ATPase_AAA_core domain-containing protein.	0.615
A0A0M3R849	A0A2C9WEK2	A0A0M3R849	A0A2C9WEK2	NAC transcription factors 3.	AAA domain-containing protein.	0.414
A0A0M3R849	A0A2C9WLH4	A0A0M3R849	A0A2C9WLH4	NAC transcription factors 3.	Proliferating cell nuclear antigen; This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand; Belongs to the PCNA family.	0.714
A0A0M3R849	A0A2C9WN70	A0A0M3R849	A0A2C9WN70	NAC transcription factors 3.	Uncharacterized protein.	0.469
A0A0M4G3S7	A0A251JWR0	A0A0M4G3S7	A0A251JWR0	NAC transcription factors 94.	DNA ligase.	0.420