Editing Interactome (section)

==Studied interactomes==

===Viral interactomes===
Viral protein interactomes consist of interactions among viral or phage proteins. They were among the first interactome projects as their genomes are small and all proteins can be analyzed with limited resources. Viral interactomes are connected to their host interactomes, forming virus-host interaction networks.<ref>{{cite journal |author=Navratil V.|title=VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks|journal=Nucleic Acids Res.|volume=37 |pages=D661–8|year=2009 |pmid= 18984613 |doi=10.1093/nar/gkn794 |last2=De Chassey |first2=B. |last3=Meyniel |first3=L. |last4=Delmotte |first4=S. |last5=Gautier |first5=C. |last6=Andre |first6=P. |last7=Lotteau |first7=V. |last8=Rabourdin-Combe |first8=C. |issue=Database issue |pmc=2686459|display-authors=1}}</ref> Some published virus interactomes include

'''Bacteriophage'''
* ''[[Escherichia coli]]'' [[Lambda phage|bacteriophage lambda]]<ref>{{cite journal |author=Rajagopala SV.|title=The protein interaction map of bacteriophage lambda|journal= BMC Microbiol.|volume=11 |pages=213|year=2011 |pmid= 21943085 |doi=10.1186/1471-2180-11-213 |pmc=3224144 |last2=Casjens |first2=Sherwood |last3=Uetz |first3=Peter|display-authors=1 |doi-access=free }} {{open access}}</ref>
* ''[[Escherichia coli]]'' [[T7 phage|bacteriophage T7]]<ref name="pmid8528255">{{cite journal |vauthors=Bartel PL, Roecklein JA, SenGupta D, Fields S |title=A protein linkage map of Escherichia coli bacteriophage T7 |journal=Nat. Genet. |volume=12 |issue=1 |pages=72–7 |year=1996 |pmid=8528255 |doi=10.1038/ng0196-72 |s2cid=37155819 }}</ref>
* ''[[Streptococcus pneumoniae]]'' bacteriophage Dp-1<ref>{{cite journal |author=Sabri M.|title=Genome annotation and intraviral interactome for the ''Streptococcus pneumoniae'' virulent phage Dp-1|journal=J. Bacteriol.|volume=193 |pages=551–62|year=2011 |pmid= 21097633 |doi=10.1128/JB.01117-10 |pmc=3019816 |issue=2 |last2=Hauser |first2=R. |last3=Ouellette |first3=M. |last4=Liu |first4=J. |last5=Dehbi |first5=M. |last6=Moeck |first6=G. |last7=Garcia |first7=E. |last8=Titz |first8=B. |last9=Uetz |first9=P.|display-authors=1}}</ref>
* ''[[Streptococcus pneumoniae]]'' bacteriophage Cp-1<ref>{{cite journal |author=Häuser R.|title=The proteome and interactome of ''Streptococcus pneumoniae'' phage Cp-1|journal=J. Bacteriol.|volume=193 |pages=3135–8|year=2011 |pmid= 21515781 |doi=10.1128/JB.01481-10 |pmc=3133188 |issue=12 |last2=Sabri |first2=M. |last3=Moineau |first3=S. |last4=Uetz |first4=P.|display-authors=1}}</ref>

The lambda and VZV interactomes are not only relevant for the biology of these viruses but also for technical reasons: they were the first interactomes that were mapped with multiple [[Y2H]] vectors, proving an improved strategy to investigate interactomes more completely than previous attempts have shown.

'''Human (mammalian) viruses'''
* Human [[varicella zoster virus]] (VZV)<ref>{{cite journal|last=Stellberger|first=T.|display-authors=etal|title=Improving the yeast two-hybrid system with permutated fusions proteins: the Varicella Zoster Virus interactome|journal=Proteome Sci.|year=2010|pmid=20205919|doi=10.1186/1477-5956-8-8|pmc=2832230|volume=8|pages=8 |doi-access=free }}</ref>
* [[Chandipura virus]]<ref name="Chandipura">{{Cite journal | last1 = Kumar | first1 = K. | last2 = Rana | first2 = J. | last3 = Sreejith | first3 = R. | last4 = Gabrani | first4 = R. | last5 = Sharma | first5 = S. K. | last6 = Gupta | first6 = A. | last7 = Chaudhary | first7 = V. K. | last8 = Gupta | first8 = S. | doi = 10.1007/s00705-012-1389-5 | title = Intraviral protein interactions of Chandipura virus | journal = Archives of Virology | volume = 157 | issue = 10 | pages = 1949–1957 | year = 2012 | pmid = 22763614 | s2cid = 17714252 }}</ref>
* [[Epstein-Barr virus]] (EBV)<ref name="Fossum 2009 e1000570" />
* [[Hepatitis C virus]] (HPC),<ref name="Hagen2014">{{Cite journal | pmid = 24797426 | year = 2014 | last1 = Hagen | first1 = N | title = The intra viral protein interaction network of hepatitis C virus | journal = Molecular & Cellular Proteomics | last2 = Bayer | first2 = K | last3 = Roesch | first3 = K | last4 = Schindler | first4 = M | doi = 10.1074/mcp.M113.036301 | volume=13 | issue=7 | pages=1676–89 | doi-access = free | pmc = 4083108 }}</ref> Human-HCV interactions<ref>{{cite journal | last1 = Han | first1 = Y | last2 = Niu | first2 = J | last3 = Wang | first3 = D | last4 = Li | first4 = Y | year = 2016 | title = Hepatitis C Virus Protein Interaction Network Analysis Based on Hepatocellular Carcinoma | journal = PLOS ONE | volume = 11 | issue = 4| page = e0153882 | doi = 10.1371/journal.pone.0153882| pmid = 27115606 | pmc = 4846009 | bibcode = 2016PLoSO..1153882H | doi-access = free }}</ref>
* [[Hepatitis E virus]] (HEV)<ref name="pmid26463011">{{cite journal |vauthors=Osterman A, Stellberger T, Gebhardt A, Kurz M, Friedel CC, Uetz P, Nitschko H, Baiker A, Vizoso-Pinto MG |title=The Hepatitis E virus intraviral interactome |journal=Sci Rep |volume=5 |pages=13872 |year=2015 |pmid=26463011 |pmc=4604457 |doi=10.1038/srep13872 |bibcode=2015NatSR...513872O }}</ref>
* [[Herpes simplex virus 1]] (HSV-1)<ref name="Fossum 2009 e1000570" />
* [[Kaposi's sarcoma-associated herpesvirus]] (KSHV)<ref name="Fossum 2009 e1000570">{{cite journal|last=Fossum|first=E|display-authors=etal|title=Evolutionarily conserved herpesviral protein interaction networks|journal=PLOS Pathog |year=2009|pmid=19730696|doi=10.1371/journal.ppat.1000570|pmc=2731838|volume=5|issue=9|pages=e1000570|editor1-last=Sun|editor1-first=Ren|doi-access=free}} {{open access}}</ref>
* Murine [[cytomegalovirus]] (mCMV)<ref name="Fossum 2009 e1000570" />

===Bacterial interactomes===
Relatively few bacteria have been comprehensively studied for their protein–protein interactions. However, none of these interactomes are complete in the sense that they captured all interactions. In fact, it has been estimated that none of them covers more than 20% or 30% of all interactions, primarily because most of these studies have only employed a single method, all of which discover only a subset of interactions.<ref name="Chen">{{Cite journal
| last1 = Chen | first1 = Y. C.
| last2 = Rajagopala | first2 = S. V.
| last3 = Stellberger | first3 = T.
| last4 = Uetz | first4 = P.
| title = Exhaustive benchmarking of the yeast two-hybrid system
| doi = 10.1038/nmeth0910-667
| journal = Nature Methods
| volume = 7
| issue = 9
| pages = 667–668; author 668 668
| year = 2010
| pmid = 20805792
| s2cid = 35834541
| pmc = 10332476
}}</ref> Among the published bacterial interactomes (including partial ones) are

{| class="wikitable sortable"
! Species
! proteins total
! interactions
! type
! reference
|-
| ''[[Helicobacter pylori]]'' ||1,553||~3,004||Y2H||<ref name="Rain">{{Cite journal | last1 = Rain | first1 = J. C. | last2 = Selig | first2 = L. | last3 = De Reuse | first3 = H. | last4 = Battaglia | first4 = V. R. | last5 = Reverdy | first5 = C. L. | last6 = Simon | first6 = S. P. | last7 = Lenzen | first7 = G. | last8 = Petel | first8 = F. | last9 = Wojcik | first9 = J. R. M. | last10 = Schächter | first10 = V. | last11 = Chemama | first11 = Y. | last12 = Labigne | first12 = A. S. | last13 = Legrain | first13 = P. | title = The protein–protein interaction map of Helicobacter pylori | journal = Nature | volume = 409 | issue = 6817 | pages = 211–215 | doi = 10.1038/35051615 | year = 2001 | pmid = 11196647 
| bibcode = 2001Natur.409..211R | s2cid = 4400094 }}</ref><ref name="Häuser2014">{{Cite journal | pmid = 24627523 | year = 2014 | last1 = Häuser | first1 = R | title = A Second-generation Protein–Protein Interaction Network of Helicobacter pylori | journal = Molecular & Cellular Proteomics | last2 = Ceol | first2 = A | last3 = Rajagopala | first3 = S. V. | last4 = Mosca | first4 = R | last5 = Siszler | first5 = G | last6 = Wermke | first6 = N | last7 = Sikorski | first7 = P | last8 = Schwarz | first8 = F | last9 = Schick | first9 = M | last10 = Wuchty | first10 = S | last11 = Aloy | first11 = P | last12 = Uetz | first12 = P | doi = 10.1074/mcp.O113.033571 | volume=13 | issue=5 | pages=1318–29 | doi-access = free | pmc = 4014287 }}</ref>
|-
| ''[[Campylobacter jejuni]]''||1,623||11,687||Y2H||<ref>{{cite journal|last=Parrish|first=JR|display-authors=etal|title=A proteome-wide protein interaction map for Campylobacter jejuni|journal=Genome Biol|year=2007|pmid=17615063|doi=10.1186/gb-2007-8-7-r130|pmc=2323224|volume=8|issue=7|pages=R130 |doi-access=free }}</ref>
|-
| ''[[Treponema pallidum]]'' ||1,040||3,649||Y2H||<ref name="Titz2008">{{Cite journal | last1 = Rajagopala | first1 = S. V. | last2 = Titz | first2 = B. R. | last3 = Goll | first3 = J. | last4 = Häuser | first4 = R. | last5 = McKevitt | first5 = M. T. | last6 = Palzkill | first6 = T. | last7 = Uetz | first7 = P. | editor1-last = Hall | editor1-first = Neil | title = The Binary Protein Interactome of Treponema pallidum – the Syphilis Spirochete | doi = 10.1371/journal.pone.0002292 | journal = PLOS ONE | volume = 3 | issue = 5 | pages = e2292 | year = 2008 | pmid = 18509523 | pmc =2386257 | bibcode = 2008PLoSO...3.2292T | doi-access = free }}</ref>
|-
| ''[[Escherichia coli]]'' ||4,288||(5,993)||AP/MS||<ref>{{cite journal|last=Hu|first=P|display-authors=etal|title=Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins|journal=PLOS Biol |year=2009|pmid=19402753|doi=10.1371/journal.pbio.1000096|pmc=2672614|volume=7|issue=4|pages=e96|editor1-last=Levchenko|editor1-first=Andre|doi-access=free}} {{open access}}</ref>
|-
| ''[[Escherichia coli]]'' || 4,288 ||2,234||Y2H||<ref name="Rajagopala2014">{{Cite journal | pmid = 24561554 | year = 2014 | last1 = Rajagopala | first1 = S. V. | title = The binary protein–protein interaction landscape of Escherichia coli | journal = Nature Biotechnology | last2 = Sikorski | first2 = P | last3 = Kumar | first3 = A | last4 = Mosca | first4 = R | last5 = Vlasblom | first5 = J | last6 = Arnold | first6 = R | last7 = Franca-Koh | first7 = J | last8 = Pakala | first8 = S. B. | last9 = Phanse | first9 = S | last10 = Ceol | first10 = A | last11 = Häuser | first11 = R | last12 = Siszler | first12 = G | last13 = Wuchty | first13 = S | last14 = Emili | first14 = A | last15 = Babu | first15 = M | last16 = Aloy | first16 = P | last17 = Pieper | first17 = R | last18 = Uetz | first18 = P | doi = 10.1038/nbt.2831 | volume=32 | issue=3 | pages=285–90 | pmc=4123855 }}</ref>
|-
| ''[[Mesorhizobium loti]]'' ||6,752||3,121||Y2H||<ref name="Mloti">{{Cite journal | last1 = Shimoda | first1 = Y. | last2 = Shinpo | first2 = S. | last3 = Kohara | first3 = M. | last4 = Nakamura | first4 = Y. | last5 = Tabata | first5 = S. | last6 = Sato | first6 = S. | doi = 10.1093/dnares/dsm028 | title = A Large Scale Analysis of Protein–Protein Interactions in the Nitrogen-fixing Bacterium Mesorhizobium loti | journal = DNA Research | volume = 15 | issue = 1 | pages = 13–23 | year = 2008 | pmid = 18192278 | pmc =2650630 }}</ref>
|-
| ''[[Mycobacterium tuberculosis]]'' ||3,959||>8000||B2H||<ref name="Mtub">{{Cite journal | last1 = Wang | first1 = Y. | last2 = Cui | first2 = T. | last3 = Zhang | first3 = C. | last4 = Yang | first4 = M. | last5 = Huang | first5 = Y. | last6 = Li | first6 = W. | last7 = Zhang | first7 = L. | last8 = Gao | first8 = C. | last9 = He | first9 = Y. | last10 = Li | doi = 10.1021/pr100808n | first10 = Y. | last11 = Huang | first11 = F. | last12 = Zeng | first12 = J. | last13 = Huang | first13 = C. | last14 = Yang | first14 = Q. | last15 = Tian | first15 = Y. | last16 = Zhao | first16 = C. | last17 = Chen | first17 = H. | last18 = Zhang | first18 = H. | last19 = He | first19 = Z. G. | title = Global Protein−Protein Interaction Network in the Human PathogenMycobacterium tuberculosisH37Rv | journal = Journal of Proteome Research | volume = 9 | issue = 12 | pages = 6665–6677 | year = 2010 | pmid = 20973567 }}</ref>
|-
| ''[[Mycoplasma genitalium]]'' ||482||||AP/MS||<ref name="Myco">{{Cite journal | last1 = Kuhner | first1 = S. | last2 = Van Noort | first2 = V. | last3 = Betts | first3 = M. J. | last4 = Leo-Macias | first4 = A. | last5 = Batisse | first5 = C. | last6 = Rode | first6 = M. | last7 = Yamada | first7 = T. | last8 = Maier | first8 = T. | last9 = Bader | first9 = S. | doi = 10.1126/science.1176343 | last10 = Beltran-Alvarez | first10 = P. | last11 = Castaño-Diez | first11 = D. | last12 = Chen | first12 = W. -H. | last13 = Devos | first13 = D. | last14 = Güell | first14 = M. | last15 = Norambuena | first15 = T. | last16 = Racke | first16 = I. | last17 = Rybin | first17 = V. | last18 = Schmidt | first18 = A. | last19 = Yus | first19 = E. | last20 = Aebersold | first20 = R. | last21 = Herrmann | first21 = R. | last22 = Böttcher | first22 = B. | last23 = Frangakis | first23 = A. S. | last24 = Russell | first24 = R. B. | last25 = Serrano | first25 = L. | last26 = Bork | first26 = P. | last27 = Gavin | first27 = A. -C. | title = Proteome Organization in a Genome-Reduced Bacterium | journal = Science | volume = 326 | issue = 5957 | pages = 1235–1240 | year = 2009 | pmid = 19965468 | bibcode = 2009Sci...326.1235K | s2cid = 19334426 }}</ref>
|-
| ''[[Synechocystis]]'' sp. PCC6803 ||3,264||3,236||Y2H||<ref name="Sato">{{Cite journal | last1 = Sato | first1 = S. | last2 = Shimoda | first2 = Y. | last3 = Muraki | first3 = A. | last4 = Kohara | first4 = M. | last5 = Nakamura | first5 = Y. | last6 = Tabata | first6 = S. | doi = 10.1093/dnares/dsm021 | title = A Large-scale Protein protein Interaction Analysis in Synechocystis sp. PCC6803 | journal = DNA Research | volume = 14 | issue = 5 | pages = 207–216 | year = 2007 | pmid = 18000013 | pmc =2779905 }}</ref>
|-
| ''[[Staphylococcus aureus]]'' (MRSA) ||2,656||13,219||AP/MS||<ref name="Cherkasov">{{Cite journal | pmid = 21166474 | year = 2011 | last1 = Cherkasov | first1 = A | title = Mapping the protein interaction network in methicillin-resistant ''Staphylococcus aureus'' | journal = Journal of Proteome Research | volume = 10 | issue = 3 | pages = 1139–50 | last2 = Hsing | first2 = M | last3 = Zoraghi | first3 = R | last4 = Foster | first4 = L. J. | last5 = See | first5 = R. H. | last6 = Stoynov | first6 = N | last7 = Jiang | first7 = J | last8 = Kaur | first8 = S | last9 = Lian | first9 = T | last10 = Jackson | first10 = L | last11 = Gong | first11 = H | last12 = Swayze | first12 = R | last13 = Amandoron | first13 = E | last14 = Hormozdiari | first14 = F | last15 = Dao | first15 = P | last16 = Sahinalp | first16 = C | last17 = Santos-Filho | first17 = O | last18 = Axerio-Cilies | first18 = P | last19 = Byler | first19 = K | last20 = McMaster | first20 = W. R. | last21 = Brunham | first21 = R. C. | last22 = Finlay | first22 = B. B. | last23 = Reiner | first23 = N. E. | doi = 10.1021/pr100918u }}</ref>
|}

The ''E. coli'' and ''Mycoplasma'' interactomes have been analyzed using large-scale protein complex affinity purification and mass spectrometry (AP/MS), hence it is not easily possible to infer direct interactions. The others have used extensive [[yeast two-hybrid]] (Y2H) screens. The ''Mycobacterium tuberculosis'' interactome has been analyzed using a [[bacterial two-hybrid screen]] (B2H).

Note that numerous additional interactomes have been predicted using computational methods (see section above).

===Eukaryotic interactomes===
There have been several efforts to map eukaryotic interactomes through HTP methods. While no biological interactomes have been fully characterized, over 90% of proteins in ''Saccharomyces cerevisiae'' have been screened and their interactions characterized, making it the best-characterized interactome.<ref name="Schwikowski2000"/><ref name="Uetz2000">{{Cite journal | last1 = Uetz | first1 = P. | last2 = Giot | first2 = L. | last3 = Cagney | first3 = G. | last4 = Mansfield | first4 = T. A. | last5 = Judson | first5 = R. S. | last6 = Knight | first6 = J. R. | last7 = Lockshon | first7 = D. | last8 = Narayan | first8 = V. | title = A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae | journal = Nature | volume = 403 | issue = 6770 | pages = 623–627 | doi = 10.1038/35001009 | year = 2000 | pmid = 10688190 | bibcode = 2000Natur.403..623U | s2cid = 4352495 }}</ref><ref>{{cite journal |last =Krogan |first= NJ |display-authors=etal | year=2006|title = Global landscape of protein complexes in the yeast ''Saccharomyeses Cerivisiae ''| journal = Nature| volume= 440 |pages = 637–643|doi = 10.1038/nature04670 |pmid =16554755|issue =7084|bibcode=2006Natur.440..637K|s2cid= 72422 }}</ref> Species whose interactomes have been studied in some detail include 
* ''[[Schizosaccharomyces pombe]]''<ref name="pmid22540037">{{cite journal |vauthors=Pancaldi V, Saraç OS, Rallis C, McLean JR, Převorovský M, Gould K, Beyer A, Bähler J |title=Predicting the fission yeast protein interaction network |journal=G3: Genes, Genomes, Genetics |volume=2 |issue=4 |pages=453–67 |year=2012 |pmid=22540037 |pmc=3337474 |doi=10.1534/g3.111.001560 }}</ref><ref>{{cite journal | last1 = Vo | first1 = T.V. | display-authors = etal |year = 2016 | title = A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human | journal = Cell | volume = 164 | issue = 1–2| pages = 310–323 | doi = 10.1016/j.cell.2015.11.037 | pmid = 26771498 | pmc = 4715267}}</ref>
* ''[[Caenorhabditis elegans]]''
* ''[[Drosophila melanogaster]]''
* ''Homo sapiens''
Recently, the pathogen-host interactomes of Hepatitis C Virus/Human (2008),<ref name="hcv">{{cite journal |author=de Chassey B |title=Hepatitis C virus infection protein network |journal=Molecular Systems Biology |date=2008-11-04 |volume=4 |issue= 4 |page=230 |pmid=18985028 |pmc=2600670 |doi=10.1038/msb.2008.66|author2= Navratil V |author3= Tafforeau L |display-authors=etal}}</ref> Epstein Barr virus/Human (2008), Influenza virus/Human (2009) were delineated through HTP to identify essential molecular components for pathogens and for their host's immune system.<ref name="vin">{{cite journal |author=Navratil V |title=Systems-level comparison of protein–protein interactions between viruses and the human type I interferon system network|journal=Journal of Proteome Research |volume=9 |issue=7 |pages=3527–36 |date=2010-11-05|pmid=20459142 |doi=10.1021/pr100326j|author2= de Chassey B|display-authors=etal}}</ref>

===Predicted interactomes===
As described above, PPIs and thus whole interactomes can be predicted. While the reliability of these predictions is debatable, they are providing hypotheses that can be tested experimentally. Interactomes have been predicted for a number of species, e.g.
* Human (''[[Homo sapiens]]'')<ref name="pmid15657099">{{cite journal |vauthors=Brown KR, Jurisica I |title=Online predicted human interaction database |journal=Bioinformatics |volume=21 |issue=9 |pages=2076–82 |year=2005 |pmid=15657099 |doi=10.1093/bioinformatics/bti273 |doi-access=free }}</ref>
* Rice (''[[Oryza sativa]]'')<ref name="pmid21575196">{{cite journal |vauthors=Gu H, Zhu P, Jiao Y, Meng Y, Chen M |title=PRIN: a predicted rice interactome network |journal=BMC Bioinformatics |volume=12 |pages=161 |year=2011 |pmid=21575196 |pmc=3118165 |doi=10.1186/1471-2105-12-161 |doi-access=free }}</ref>
* ''[[Xanthomonas oryzae]]''<ref name="pmid24113387">{{cite journal |vauthors=Guo J, Li H, Chang JW, Lei Y, Li S, Chen LL |title=Prediction and characterization of protein–protein interaction network in Xanthomonas oryzae pv. oryzae PXO99 A |journal=Res. Microbiol. |volume=164 |issue=10 |pages=1035–44 |year=2013 |pmid=24113387 |doi=10.1016/j.resmic.2013.09.001 |doi-access=free }}</ref>
* ''[[Arabidopsis thaliana]]''<ref name="pmid17675552">{{cite journal |vauthors=Geisler-Lee J, O'Toole N, Ammar R, Provart NJ, Millar AH, Geisler M |title=A predicted interactome for Arabidopsis |journal=Plant Physiol. |volume=145 |issue=2 |pages=317–29 |year=2007 |pmid=17675552 |pmc=2048726 |doi=10.1104/pp.107.103465 }}</ref>
* Tomato (''[[Solanum lycopersicum]]'')<ref>{{Cite journal|last1=Yue|first1=Junyang|last2=Xu|first2=Wei|last3=Ban|first3=Rongjun|last4=Huang|first4=Shengxiong|last5=Miao|first5=Min|last6=Tang|first6=Xiaofeng|last7=Liu|first7=Guoqing|last8=Liu|first8=Yongsheng|date=2016-01-01|title=PTIR: Predicted Tomato Interactome Resource|journal=Scientific Reports|volume=6|pages=25047|doi=10.1038/srep25047|issn=2045-2322|pmid=27121261|pmc=4848565|bibcode=2016NatSR...625047Y}}</ref>
* Field mustard (''[[Brassica rapa]]'')<ref>{{Cite journal|last1=Yang|first1=Jianhua|last2=Osman|first2=Kim|last3=Iqbal|first3=Mudassar|last4=Stekel|first4=Dov J.|last5=Luo|first5=Zewei|last6=Armstrong|first6=Susan J.|last7=Franklin|first7=F. Chris H.|date=2012-01-01|title=Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana|journal=Frontiers in Plant Science|volume=3|pages=297|doi=10.3389/fpls.2012.00297|issn=1664-462X|pmc=3537189|pmid=23293649|doi-access=free}}</ref> 
* ''Maize, corn ([[Maize|Zea mays]])''<ref>{{Cite journal|last1=Zhu|first1=Guanghui|last2=Wu|first2=Aibo|last3=Xu|first3=Xin-Jian|last4=Xiao|first4=Pei-Pei|last5=Lu|first5=Le|last6=Liu|first6=Jingdong|last7=Cao|first7=Yongwei|last8=Chen|first8=Luonan|last9=Wu|first9=Jun|date=2016-02-01|title=PPIM: A Protein–Protein Interaction Database for Maize|journal=Plant Physiology|volume=170|issue=2|pages=618–626|doi=10.1104/pp.15.01821|issn=1532-2548|pmc=4734591|pmid=26620522}}</ref>
* Poplar (''[[Populus trichocarpa]]'')<ref>{{Cite journal|last1=Rodgers-Melnick|first1=Eli|last2=Culp|first2=Mark|last3=DiFazio|first3=Stephen P.|date=2013-01-01|title=Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS|journal=BMC Genomics|volume=14|pages=608|doi=10.1186/1471-2164-14-608|issn=1471-2164|pmc=3848842|pmid=24015873 |doi-access=free }}</ref>
* ''[[SARS-CoV-2]]''<ref name="pmid32244779">{{cite journal |vauthors=Guzzi PH, Mercatelli D, Ceraolo C, Giorgi FM |title=Master Regulator Analysis of the SARS-CoV-2/Human Interactome |journal=Journal of Clinical Medicine |volume=9 |issue=4 |pages=982–988 |year=2020 |pmid=32244779 |doi=10.3390/jcm9040982 |pmc=7230814 |doi-access=free }}</ref>
[[File:Figure1 interactome highres.tif|thumb|Representation of the predicted SARS-CoV-2/Human interactome<ref name="pmid32244779"/>]]