Organism : Clostridium acetobutylicum | Module List :
CAC0682 nrgA

Ammonium transporter (membrane protein nrgA) (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Ammonia permease cog/ cog
transport go/ biological_process
ammonium transmembrane transporter activity go/ molecular_function
membrane go/ cellular_component
amt tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0682
(Mouseover regulator name to see its description)

CAC0682 is regulated by 27 influences and regulates 0 modules.
Regulators for CAC0682 nrgA (27)
Regulator Module Operator
CAC0144 8 tf
CAC0265 8 tf
CAC0284 8 tf
CAC0379 8 tf
CAC0461 8 tf
CAC0766 8 tf
CAC0977 8 tf
CAC1463 8 tf
CAC1753 8 tf
CAC2074 8 tf
CAC3104 8 tf
CAC3200 8 tf
CAC3731 8 tf
CAC0019 297 tf
CAC0144 297 tf
CAC0255 297 tf
CAC0265 297 tf
CAC0284 297 tf
CAC0707 297 tf
CAC0766 297 tf
CAC1333 297 tf
CAC1928 297 tf
CAC2074 297 tf
CAC2113 297 tf
CAC2476 297 tf
CAC3143 297 tf
CAC3149 297 tf

Warning: CAC0682 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
6670 1.20e+02 AagAggAaGag
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6671 7.40e+02 GCagGagG
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7246 8.40e+01 aGGagG
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7247 1.20e+03 ggGtatagcgtTTcTAtC
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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 CAC0682

CAC0682 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Ammonia permease cog/ cog
transport go/ biological_process
ammonium transmembrane transporter activity go/ molecular_function
membrane go/ cellular_component
amt tigr/ tigrfam
Module neighborhood information for CAC0682

CAC0682 has total of 36 gene neighbors in modules 8, 297
Gene neighbors (36)
Gene Common Name Description Module membership
CAC0008 CAC0008 Predicted HD superfamily hydrolase (NCBI ptt file) 8, 130
CAC0028 hydA Hydrogene dehydrogenase (NCBI ptt file) 8, 130
CAC0077 CAC0077 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 297, 317
CAC0616 CAC0616 Predicted membrane protein (NCBI ptt file) 8, 162
CAC0682 nrgA Ammonium transporter (membrane protein nrgA) (NCBI ptt file) 8, 297
CAC0683 CAC0683 Hypothetical protein (NCBI ptt file) 8, 215
CAC0744 CAC0744 Na+/H+ antiporter, ortholog YQKI B.subtilis (NCBI ptt file) 252, 297
CAC0767 CAC0767 Fe-S oxidoreductase (NCBI ptt file) 8, 116
CAC0775 CAC0775 ATP-utilizing enzyme of the PP-loop superfamily (NCBI ptt file) 8, 130
CAC1097 CAC1097 Hypothetical protein (NCBI ptt file) 297, 317
CAC1307 CAC1307 Hypothetical protein (NCBI ptt file) 51, 297
CAC1611 CAC1611 Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file) 8, 297
CAC1720 CAC1720 Flavoprotein involved in panthothenate metabolism, YLOI B.subtilis ortholog (NCBI ptt file) 8, 172
CAC1757 CAC1757 RimM protein, required for 16S rRNA processing (NCBI ptt file) 76, 297
CAC1758 trmD TRNA-(guanine-N1)-methyltransferase, TrmD (NCBI ptt file) 76, 297
CAC1821 purB Adenylosuccinate lyase (NCBI ptt file) 106, 297
CAC2265 CAC2265 Uncharacterized conserved membrane protein (NCBI ptt file) 106, 297
CAC2266 CAC2266 Uncharacterized conserved membrane protein (fragment) (NCBI ptt file) 106, 297
CAC2277 secF Preprotein translocase subunit SecF (NCBI ptt file) 8, 149
CAC2278 secD Preprotein translocase subunits SecD (NCBI ptt file) 8, 179
CAC2279 CAC2279 Heme biosynthesis (nirJ-2) family protein (NCBI ptt file) 8, 179
CAC2312 CAC2312 Rhamnosyl transferase, rfbQ (NCBI ptt file) 8, 130
CAC2313 CAC2313 Glycosyltransferase (NCBI ptt file) 8, 130
CAC2314 CAC2314 Membrane protein involved in the export of O-antigen and teichoic acid, RfbX family (NCBI ptt file) 8, 130
CAC2374 oppC Oligopeptide ABC-type transporter, permease component OPPC (NCBI ptt file) 224, 297
CAC2375 oppB Oligopeptide ABC-type transporter, permease (NCBI ptt file) 224, 297
CAC2398 folC Folylpolyglutamate synthase (NCBI ptt file) 296, 297
CAC2399 vals Valyl-tRNA synthetase (NCBI ptt file) 296, 297
CAC2849 CAC2849 Proline/glycine betaine ABC-type transport system, permease component fused to periplasmic component (NCBI ptt file) 8, 297
CAC2850 CAC2850 Proline/glycine betaine ABC-type transport system, ATPase component (NCBI ptt file) 8, 84
CAC2925 CAC2925 HD superfamily hydrolase (NCBI ptt file) 286, 297
CAC2926 sul Dihydropteroate synthase (NCBI ptt file) 34, 297
CAC2927 folA/folK Dihydroneopterin aldolase fused to 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (NCBI ptt file) 286, 297
CAC3104 rpoA DNA-dependent RNA polymerase alpha subunit (NCBI ptt file) 8, 304
CAC3262 CAC3262 ATPase with chaperone activity, ATP-binding domain, diverged (NCBI ptt file) 224, 297
CAC3390 CAC3390 Response regulator (CheY-like receiver domain containing) (NCBI ptt file) 51, 297
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 CAC0682
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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