Organism : Geobacter sulfurreducens | Module List :
GSU3066 ddl

D-alanine--D-alanine ligase (NCBI)

CircVis
Functional Annotations (10)
Function System
D-alanine-D-alanine ligase and related ATP-grasp enzymes cog/ cog
ATP binding go/ molecular_function
cell wall go/ cellular_component
cytoplasm go/ cellular_component
D-alanine-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
D-Alanine metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
D_ala_D_alaTIGR tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3066
(Mouseover regulator name to see its description)

GSU3066 is regulated by 18 influences and regulates 0 modules.
Regulators for GSU3066 ddl (18)
Regulator Module Operator
GSU0041 264 tf
GSU1320 264 tf
GSU1569 264 tf
GSU1639 264 tf
GSU1992 264 tf
GSU2735 264 tf
GSU2809 264 tf
GSU2868 264 tf
GSU2915 264 tf
GSU0164 35 tf
GSU0300 35 tf
GSU1003 35 tf
GSU1250 35 tf
GSU1863 35 tf
GSU2571 35 tf
GSU2625 35 tf
GSU3206 35 tf
GSU3217 35 tf

Warning: GSU3066 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
2230 1.50e+01 Aat.c.tTgaAAAA.
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2231 3.10e+03 CTGATTTT
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2688 1.80e+02 AAaAAT
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2689 2.50e+03 tgtcatAaaAaaGattactT
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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 GSU3066

GSU3066 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
D-alanine-D-alanine ligase and related ATP-grasp enzymes cog/ cog
ATP binding go/ molecular_function
cell wall go/ cellular_component
cytoplasm go/ cellular_component
D-alanine-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
D-Alanine metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
D_ala_D_alaTIGR tigr/ tigrfam
Module neighborhood information for GSU3066

GSU3066 has total of 56 gene neighbors in modules 35, 264
Gene neighbors (56)
Gene Common Name Description Module membership
GSU0006 gpsA glycerol-3-phosphate dehydrogenase (NAD(P)+) (NCBI) 35, 254
GSU0098 GSU0098 MglB protein (VIMSS) 114, 264
GSU0145 recA recA protein (NCBI) 35, 233
GSU0180 GSU0180 conserved hypothetical protein (VIMSS) 35, 202
GSU0303 GSU0303 sensory box protein (VIMSS) 22, 35
GSU0335 GSU0335 hypothetical protein (VIMSS) 35, 170
GSU0388 GSU0388 conserved hypothetical protein (NCBI) 89, 264
GSU0476 GSU0476 conserved hypothetical protein (VIMSS) 77, 264
GSU0511 GSU0511 conserved domain protein (NCBI) 35, 231
GSU0661 prsA ribose-phosphate pyrophosphokinase (NCBI) 35, 81
GSU0664 ychF GTP binding protein YchF (NCBI) 35, 161
GSU0780 GSU0780 formate dehydrogenase accessory protein FdhD (VIMSS) 184, 264
GSU0888 GSU0888 hypothetical protein (NCBI) 35, 202
GSU1073 GSU1073 conserved hypothetical protein (VIMSS) 35, 260
GSU1117 GSU1117 response regulator (VIMSS) 94, 264
GSU1118 GSU1118 universal stress protein family (VIMSS) 264, 276
GSU1119 GSU1119 sensor histidine kinase/response regulator (VIMSS) 94, 264
GSU1230 GSU1230 conserved hypothetical protein (VIMSS) 35, 205
GSU1234 sppA-2 signal peptide peptidase SppA, 36K type (NCBI) 35, 88
GSU1292 GSU1292 sensory box histidine kinase (VIMSS) 35, 295
GSU1459 ispG 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (NCBI) 35, 245
GSU1598 GSU1598 conserved hypothetical protein (NCBI) 35, 267
GSU1639 GSU1639 Rrf2 family protein (NCBI) 264, 315
GSU1640 cydA cytochrome d ubiquinol oxidase, subunit I (NCBI) 264, 315
GSU1641 cydB cytochrome d ubiquinol oxidase, subunit II (NCBI) 264, 315
GSU1672 hprA glycerate dehydrogenase (NCBI) 35, 314
GSU1795 rph ribonuclease PH (NCBI) 35, 158
GSU1817 GSU1817 outer membrane lipoprotein, Slp family, putative (VIMSS) 53, 264
GSU1825 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (VIMSS) 35, 267
GSU1867 GSU1867 hypothetical protein (VIMSS) 258, 264
GSU1949 GSU1949 hypothetical protein (VIMSS) 65, 264
GSU1992 GSU1992 transcriptional regulator, Crp/Fnr family (VIMSS) 264, 279
GSU1996 GSU1996 cytochrome c family protein (NCBI) 35, 154
GSU2044 GSU2044 sensory box/GGDEF family protein (VIMSS) 100, 264
GSU2234 rpmB ribosomal protein L28 (NCBI) 35, 340
GSU2730 GSU2730 hypothetical protein (NCBI) 113, 264
GSU2807 GSU2807 conserved hypothetical protein (VIMSS) 35, 202
GSU3013 cgpA GTP-binding protein (NCBI) 19, 35
GSU3063 ftsZ cell division protein FtsZ (NCBI) 230, 264
GSU3065 ftsQ cell division protein FtsQ (NCBI) 200, 264
GSU3066 ddl D-alanine--D-alanine ligase (NCBI) 35, 264
GSU3067 murB UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI) 94, 264
GSU3068 murC UDP-N-acetylmuramate--alanine ligase (NCBI) 94, 264
GSU3069 murG UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI) 140, 264
GSU3070 GSU3070 cell division protein, rodA/ftsW/spoVE family (VIMSS) 60, 264
GSU3071 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI) 95, 264
GSU3072 mraY phospho-N-acetylmuramoyl-pentapeptide-transferase (NCBI) 140, 264
GSU3117 ssb-2 single-strand binding protein (NCBI) 35, 228
GSU3132 huP-2 DNA-binding protein HU (NCBI) 35, 116
GSU3206 dksA dnaK suppressor protein, putative (NCBI) 18, 35
GSU3238 GSU3238 Rieske 2Fe-2S family protein (VIMSS) 95, 264
GSU3240 GSU3240 radical SAM domain protein (NCBI) 100, 264
GSU3246 GSU3246 thioredoxin peroxidase (VIMSS) 264, 315
GSU3260 GSU3260 phosphoserine aminotransferase, putative (VIMSS) 35, 126
GSU3292 GSU3292 transcriptional regulator, Fur family (VIMSS) 35, 202
GSU3293 GSU3293 conserved hypothetical protein (VIMSS) 35, 315
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 GSU3066
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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