Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_2436

peptide methionine sulfoxide reductase (EC:1.8.4.11)

CircVis
Functional Annotations (4)
Function System
Peptide methionine sulfoxide reductase cog/ cog
peptide-methionine-(S)-S-oxide reductase activity go/ molecular_function
protein metabolic process go/ biological_process
msrA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_2436
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_2436!

Warning: Synpcc7942_2436 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
1757 2.60e+02 tACCCtAgcaaaga
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1758 4.50e+02 aaG.TCaAatgCTtaAcA.t
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1759 1.20e+04 TCTGCtaAGCT
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1883 5.20e+00 tgccaatttCCcGaaAAacT
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1884 2.00e+02 tAAaAGttCTGaGctAGacaaGgC
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1885 9.90e+03 TcgcCaaGAccTGac
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for Synpcc7942_2436

Synpcc7942_2436 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Peptide methionine sulfoxide reductase cog/ cog
peptide-methionine-(S)-S-oxide reductase activity go/ molecular_function
protein metabolic process go/ biological_process
msrA tigr/ tigrfam
Module neighborhood information for Synpcc7942_2436

Synpcc7942_2436 has total of 57 gene neighbors in modules 79, 122
Gene neighbors (57)
Gene Common Name Description Module membership
Synpcc7942_0012 rpsF SSU ribosomal protein S6P (IMGterm) 122, 181
Synpcc7942_0044 hypothetical protein 102, 122
Synpcc7942_0050 hypothetical protein 61, 122
Synpcc7942_0103 Ankyrin 23, 79
Synpcc7942_0153 hypothetical protein 88, 122
Synpcc7942_0164 Iojap-related protein 122, 181
Synpcc7942_0166 asparaginase (EC 3.5.1.1) (IMGterm) 43, 122
Synpcc7942_0356 conserved hypothetical protein YCF33 112, 122
Synpcc7942_0372 hypothetical protein 55, 79
Synpcc7942_0388 probable glycosyltransferase 79, 153
Synpcc7942_0419 biotin synthase (EC 2.8.1.6) (IMGterm) 65, 122
Synpcc7942_0464 hypothetical protein 2, 122
Synpcc7942_0477 conserved hypothetical protein YCF19 88, 122
Synpcc7942_0525 aroB 3-dehydroquinate synthase (EC 4.2.3.4) (IMGterm) 79, 206
Synpcc7942_0667 hypothetical protein 88, 122
Synpcc7942_0669 DNA-3-methyladenine glycosylase (EC:3.2.2.21) 32, 122
Synpcc7942_0670 pyrB aspartate carbamoyltransferase (EC 2.1.3.2) (IMGterm) 32, 122
Synpcc7942_0787 putative purple acid phosphatase (EC:3.1.3.2) 88, 122
Synpcc7942_0815 neutral amino acid ABC transporter ATP-binding protein (IMGterm) 69, 79
Synpcc7942_0916 hypothetical protein 10, 122
Synpcc7942_0957 "cob(I)yrinic acid a,c-diamide adenosyltransferase (EC 2.5.1.17) (IMGterm)" 107, 122
Synpcc7942_0990 cobU adenosylcobinamide kinase (EC 2.7.1.156) (IMGterm) 23, 79
Synpcc7942_1006 TPR repeat 65, 122
Synpcc7942_1127 microcin-processing peptidase 2. Unknown type peptidase. MEROPS family U62 (IMGterm) 122, 181
Synpcc7942_1130 protein serine/threonine phosphatase (IMGterm) 4, 122
Synpcc7942_1221 response regulator receiver domain protein (CheY-like) 2, 122
Synpcc7942_1355 response regulator receiver modulated diguanylate cyclase/phosphodiesterase with PAS/PAC sensor(s) (IMGterm) 55, 79
Synpcc7942_1356 response regulator receiver domain protein (CheY-like) 55, 79
Synpcc7942_1467 Heat shock protein DnaJ-like 19, 79
Synpcc7942_1478 cytochrome CytM 12, 122
Synpcc7942_1519 hisD histidinol dehydrogenase (EC 1.1.1.23) (IMGterm) 122, 198
Synpcc7942_1600 "5',5'''-P-1,P-4-tetraphosphate phosphorylase II-like (EC:2.7.7.53)" 83, 122
Synpcc7942_1710 RNA polymerase subunit omega (rpoZ) (EC:2.7.7.6) 122, 181
Synpcc7942_1720 hypothetical protein 13, 122
Synpcc7942_1775 phosphate starvation-induced protein 79, 206
Synpcc7942_1780 mutL DNA mismatch repair protein MutL (IMGterm) 22, 79
Synpcc7942_1790 DNA adenine methylase (EC:2.1.1.72) 79, 206
Synpcc7942_1796 hypothetical protein 102, 122
Synpcc7942_1891 hypothetical protein 112, 122
Synpcc7942_1893 neutral amino acid ABC transporter ATP-binding protein (IMGterm) 79, 124
Synpcc7942_1899 hypothetical protein 23, 79
Synpcc7942_2060 hypothetical protein 30, 122
Synpcc7942_2116 hypothetical protein 9, 79
Synpcc7942_2117 gatA aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-) (IMGterm) 20, 79
Synpcc7942_2180 bacterioferritin comigratory protein (EC:1.11.1.15) 107, 122
Synpcc7942_2250 recF DNA replication and repair protein RecF 79, 206
Synpcc7942_2320 hypothetical protein 122, 160
Synpcc7942_2329 metal dependent phosphohydrolase (IMGterm) 15, 79
Synpcc7942_2436 peptide methionine sulfoxide reductase (EC:1.8.4.11) 79, 122
Synpcc7942_2444 "phosphate ABC transporter substrate-binding protein, PhoT family (TC 3.A.1.7.1) (IMGterm)" 32, 79
Synpcc7942_2504 hypothetical protein 32, 79
Synpcc7942_2528 hypothetical protein 79, 124
Synpcc7942_2552 hydrogenase accessory protein HypB 54, 79
Synpcc7942_2561 Delta-9 acyl-phospholipid desaturase (EC 1.14.19.-) (IMGterm) 77, 122
Synpcc7942_2578 hypothetical protein 95, 122
Synpcc7942_2580 Heat shock protein Hsp70 88, 122
Synpcc7942_2597 adenylate cyclase (IMGterm) 55, 79
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for Synpcc7942_2436
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend