Organism : Geobacter sulfurreducens | Module List :
GSU2079 mrdA

penicillin-binding protein 2 (NCBI)

CircVis
Functional Annotations (6)
Function System
Cell division protein FtsI/penicillin-binding protein 2 cog/ cog
penicillin binding go/ molecular_function
peptidoglycan glycosyltransferase activity go/ molecular_function
peptidoglycan-based cell wall biogenesis go/ biological_process
Peptidoglycan biosynthesis kegg/ kegg pathway
pbp2_mrdA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2079
(Mouseover regulator name to see its description)

GSU2079 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU2079 mrdA (19)
Regulator Module Operator
GSU0031 7 tf
GSU0280 7 tf
GSU0366 7 tf
GSU0581 7 tf
GSU1495 7 tf
GSU1522 7 tf
GSU2625 7 tf
GSU2753 7 tf
GSU3298 7 tf
GSU0013 67 tf
GSU0041 67 tf
GSU0280 67 tf
GSU1013 67 tf
GSU1495 67 tf
GSU1569 67 tf
GSU1626 67 tf
GSU1727 67 tf
GSU1989 67 tf
GSU2581 67 tf

Warning: GSU2079 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2174 6.00e+03 GAAataAa
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2175 3.40e+04 ATAAta.a.aagCAtCcgtg.gGa
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2294 3.90e+00 C.CcCccTcCaccc.cCcGgC
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2295 5.20e+01 AAAATcACctGAaaa
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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 GSU2079

GSU2079 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Cell division protein FtsI/penicillin-binding protein 2 cog/ cog
penicillin binding go/ molecular_function
peptidoglycan glycosyltransferase activity go/ molecular_function
peptidoglycan-based cell wall biogenesis go/ biological_process
Peptidoglycan biosynthesis kegg/ kegg pathway
pbp2_mrdA tigr/ tigrfam
Module neighborhood information for GSU2079

GSU2079 has total of 39 gene neighbors in modules 7, 67
Gene neighbors (39)
Gene Common Name Description Module membership
GSU0117 GSU0117 aminotransferase, classes I and II (NCBI) 7, 248
GSU0328 gspE general secretion pathway protein E (NCBI) 67, 334
GSU0461 fabG-1 3-oxoacyl-(acyl carrier protein) reductase (NCBI) 67, 222
GSU0508 GSU0508 conserved hypothetical protein TIGR00247 (NCBI) 7, 121
GSU0557 GSU0557 conserved hypothetical protein, interruption-C (NCBI) 7, 68
GSU0817 GSU0817 conserved hypothetical protein (VIMSS) 7, 210
GSU1194 GSU1194 transporter, LysE family (VIMSS) 67, 112
GSU1205 GSU1205 flavodoxin family protein (VIMSS) 43, 67
GSU1208 GSU1208 membrane protein, putative (NCBI) 67, 212
GSU1244 GSU1244 methyltransferase, putative (VIMSS) 67, 334
GSU1266 lepA GTP-binding protein LepA (NCBI) 7, 176
GSU1440 GSU1440 hypothetical protein (VIMSS) 67, 139
GSU1603 fabG-2 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI) 29, 67
GSU1689 ribE riboflavin synthase, alpha subunit (NCBI) 67, 245
GSU1690 ribA 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II (NCBI) 67, 98
GSU1773 GSU1773 M23/M37 peptidase domain protein (VIMSS) 7, 83
GSU1800 GSU1800 conserved hypothetical protein TIGR00150 (VIMSS) 67, 330
GSU1803 acpS holo-(acyl-carrier-protein) synthase (NCBI) 67, 196
GSU1804 pdxJ pyridoxal phosphate biosynthetic protein PdxJ (NCBI) 67, 136
GSU1879 GSU1879 DNA-binding response regulator (VIMSS) 7, 76
GSU1914 GSU1914 membrane-associated zinc metalloprotease, putative (VIMSS) 67, 102
GSU2030 GSU2030 type IV pilus biogenesis protein PilO (VIMSS) 7, 76
GSU2031 GSU2031 type IV pilus biogenesis protein PilN (VIMSS) 7, 76
GSU2069 GSU2069 HAD-superfamily hydrolase, subfamily IA, variant 1 (NCBI) 7, 68
GSU2070 GSU2070 HNH endonuclease family protein (NCBI) 7, 68
GSU2071 rnhA ribonuclease HI (NCBI) 7, 327
GSU2072 GSU2072 1-acyl-sn-glycerol-3-phosphate acyltransferase, putative (VIMSS) 7, 248
GSU2079 mrdA penicillin-binding protein 2 (NCBI) 7, 67
GSU2081 mreC rod shape-determining protein MreC (NCBI) 7, 137
GSU2108 GSU2108 hypothetical protein (VIMSS) 67, 301
GSU2249 GSU2249 hypothetical protein (VIMSS) 67, 131
GSU2251 GSU2251 hypothetical protein (NCBI) 67, 301
GSU2266 lpxD UDP-3-O-3-hydroxymyristoyl glucosamine N-acyltransferase (VIMSS) 67, 334
GSU2356 GSU2356 hypothetical protein (VIMSS) 7, 311
GSU2547 gid gid protein (NCBI) 7, 30
GSU2548 GSU2548 hypothetical protein (VIMSS) 7, 29
GSU2555 GSU2555 melittin resistance protein, putative (NCBI) 67, 231
GSU2947 GSU2947 sensor histidine kinase (VIMSS) 67, 222
GSU3298 GSU3298 transcriptional regulator, Cro/CI family (VIMSS) 7, 248
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 GSU2079
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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