TUTORIAL


Protein-protein interaction network version 1

The protein-protein interaction (PPI) network, MePPI-In, of cassava was constructed by using cassava genome version 4.1 (Phytozome version 9.0) based on interolog method. The PPI information from seven template plants (Arabidopsis thaliana (Arabidopsis), Solanum tuberosum (potato), Zea mays (maize), Oryza sativa (rice), Ricinus communis (castor bean), Populus trichocarpa (poplar) and Glycine max (soybean) were collected from seven databases; IntAct, MINT, AtPID, AtPIN, PAIR, APID and PRIN. In addition, co-expression and domain-domain interaction (DDI) information were employed to increase the reliability of the network. The confidence scores (CV; Thanasomboon et al, 2017) represent the reliability of the predicted interaction on basis of the quality and quantity of the employed data for prediction. For interolog-based method, the confidence of the prediction was given according to the types of method for identifying the PPI in the template organism, and the number of the data leading to a PPI prediction. For DDI-based method, the potential of the predicted PPI relies on the statistical significance of the finding DDIs between a protein pair wit respect to random opportunity (see more details in Thanasomboon et al, 2017).



1
Search cassava protein by using Phytozome ID or Uniprot ID
2
Search any words in the result table

Description of terminology

Protein ID : A protein interacting with the searched protein in the formatted name as shown in Phytozome database (cassava genome version 4.1)
Other name : An alternative protein ID name in Uniprot database
Supporting evidence : Two types of information supporting each PPI (gene/protein co-expression or domain-domain interaction (DDI))
Source : Database(s) providing PPI of template plant
Template plant : Number of template plants involving in an inference of cassava PPI
No. DDI : Number of domain-domain interactions supporting each inference of cassava PPI
CV grade : Classification of predicted PPIs based on confidence level;
Basal (B) : only interolog approach inferring
High (H) : interolog approach inferring with DDI support
H1 (CV score ≥ 80th percentile)
H2 (50th ≤ CV score < 80th percentile)
H3 (CV score < 50th percentile)
CV score : Confidence value of each predicted PPI in the range of 0 to 1
CV percentile : The percentile of CV score of a predicted interaction
CV = 0 (only interolog approach inferring)
0.14 ≤ CV score ≤ 1 (H1: Highest confidence)
0.12 ≤ CV score < 0.14 (H2: very high confidence)
0.01 ≤ CV score < 0.12 (H3: High confidence)
CV percentile : The percentile of CV score of predicted interaction

Protein-protein interaction network version 2

MePPI-U, Protein-protein interaction (PPI) network of cassava, was constructed based on interolog and domain methods. This cassava PPI network is an update version of MePPI-In (Thanasomboon et al, 2017). The MePPI-U consisted of 3,638,916 interactions of 24,590 proteins covering 60 percent of proteins in cassava genome.



1
Search cassava protein by using Phytozome ID
2
Search any words in the result table

Description of terminology

Interacted Protein : the protein(s) that interact(s) with the searched protein
Definition : the definition of the interacted protein based on Arabidopsis
Prediction method : the methods that use to predict the interaction between protein pairs; I (interolog-based method), D (domain-based method) and I/D (both interolog- and domain- based method)
CV score : confidence score of predicted interaction based on number/method to identify PPI in template plant and number of domain and DDI between protein pairs.
Co-expression support : the interaction that have co-expression support information; 1 (co-expression support) and 0 (non co-expression support)

MicroRNA network

(see more details in Yawichai A, Kalapanulak S, Thammarongtham C, Saithong T (2019) Genome-Wide Identification of Putative MicroRNAs in Cassava (Manihot esculenta Crantz) and Their Functional Landscape in Cellular Regulation. BioMed Research International 2019: 2019846).


1
Search miRNA loci and location
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Display information of particular miRNA loci
3
Search miRNA loci by using gene target on Phytozome ID

Description of terminology

miRNA loci : A region of cassava genome which contains a predicted miRNA or group of miRNAs. It's compatible to "miRNA gene" or "primary miRNA". The symbol of miRNA loci herein comprises "AY" as a prefix and 7 digit numbers (for example, "AY0000001")
mature miRNA : Functional parts of miRNA loci that are able to bind miRNA targets resulting in miRNA degradation or inhibition. Mature miRNAs herein are structural predicted from stem loop structure(s) on miRNA locus. One miRNA locus can contain more than one mature miRNA. Therefor, the symbol of mature miRNA herein comprises "ay" as a prefix and the same 7 digit-number as their miRNA loci (for example, "ay0000001"). In case of more than one miRNA in miRNA locus, the symbol will be added "." and number, for example "ay0000001.1" and "ay0000001.2". The symbol will be added "-5p" or "-3p" if mature miRNAs are from both arms of duplex were predicted to function (for example, "ay0000001-5p" and "ay0000001-3p").
Family : A group of mature miRNAs that contain the similar sequences.
Mature miRNA sequence : Sequences of predicted mature miRNA
Chromosome : Location of predicted miRNAs in cassava genome version 4.1 (i.e., chromosome number, scaffold number) based on Phytozome version 11
Start : Started position of predicted mature miRNA in cassava genome version 4.1 based on Phytozome
End : Ended position of predicted mature miRNA in cassava genome version 4.1 based on Phytozome
Strand : DNA strand (sense (+) or antisense (-)) in cassava genome version 4.1 based on Phytozome

Long non-coding RNA network

The Me-lncRNAs was constructed by using cassava genome version 6.1 (Phytozome version 12.0) based on integrating of comparative- and transcriptome- based approach. Six plant genomes; Arabidopsis (Arabidopsis thaliana), Poplar (Populus trichocarpa), Castor bean (Ricinus communis), Jatropha (Jatropha curcas) and 2 cassava cultivars (W14 and KU50) were retrieved from plant genome databases for ncRNAs prediction by using comparative-based algorithm, RNAz. Seventy-four cassava RNA-seq datasets generated from 5 publications and previously published ncRNAs in RNAcentral, NCBI, GreeNC, CANTATAdb, miRbase and Rfam were used for verification. Finally, novel ncRNAs with expression supporting and passed through the filtering criteria were designated as Me-lncRNAs. Expression evidence of Me-lncRNAs indicates by number of publications supporting the expression. Of these with differential expression under cold and/or drought stress were predicted their targets based on cis- or trans- regulation.


1
Searching lncRNA loci and location
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Displaying information of particular lncRNA loci
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Finding lncRNA loci from protein-coding gene target

Description of terminology

lncRNA loci : ID of putative lncRNAs
Biotype : Types of putative lncRNAs based on genomic location including (a) lincRNA, (b) lncNAT and (c) sense/intronic lncRNA
- lincRNA : LncRNA locating at intergenic region without protein coding genes overlapping
- lncNAT : LncRNA locating at intergenic region with protein coding genes overlapping in the opposite strand
- Sense/intronic lncRNA : LncRNA located at untranslated region or intron of protein coding gene
Genome Location : Location of putative lncRNAs in cassava genome version 6.1 (i.e., chromosome, scaffold) based on Phytozome version 12
- Chromosome : Chromosome in cassava genome version 6.1 based on Phytozome version 12
- Strand : DNA strand (sense (+) or antisense (-)) in cassava genome version 6.1 based on Phytozome version 12
- Start : Started position of putative lncRNA in cassava genome version 6.1 based on Phytozome version 12
- End : End position of putative lncRNA in cassava genome version 6.1 based on Phytozome version 12
Nucleotide sequence DNA sequences of putative lncRNAs
Number of publications supporting the expression : Number of supporting putative lncRNA expression evidence (maximum is 5)
Publications : Found cassava RNA-seq datasets supporting the expression of cassava lncRNAs
  1. Li et al., 2017
  2. Pootakham et al., 2014
  3. Wilson et al., 2017
  4. Wang et al., 2014
  5. Amuge et al., 2017
Relationship : Relationship of putative lncRNA and its target genes based on cis- or trans- regulation
- Cis-regulation : Target prediction based on genomic location of protein coding gene located within 10 Kb. in up or downstream of putative lncRNA
- Trans-regulation 1 : Target prediction based on sequence complementary and normalized binding free energy (ndG) < -0.1 of putative lncRNAs and mRNA of protein coding gene target using LncTar
- Trans-regulation 2 : Target prediction based on the same mature miRNA binding with mismatch ≤ 2 of putative lncRNA and mRNA of protein coding gene target using psRNATarget
- Target gene ID : Target gene ID in cassava genome version 6.1 based on Phytozome version 12
- Condition : Condition which was found relationship between putative lncRNA and target gene including cold and/or drought stress
- miRNA : miRNA which was found to share binding region on putative lncRNA sequence and mRNA sequence of target gene