Organism : Clostridium acetobutylicum | Module List :
CAC0081 agrA

Accessory gene regulator protein A (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Response regulator of the LytR/AlgR family cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0081
(Mouseover regulator name to see its description)

CAC0081 is regulated by 13 influences and regulates 14 modules.
Regulators for CAC0081 agrA (13)
Regulator Module Operator
CAC0081 53 tf
CAC0115 53 tf
CAC0627 53 tf
CAC0708 53 tf
CAC0821 53 tf
CAC0863 53 tf
CAC0949 53 tf
CAC1320 53 tf
CAC2471 53 tf
CAC3198 53 tf
CAC3409 53 tf
CAC3673 53 tf
CAC3677 53 tf

Warning: CAC0081 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
6760 4.40e-02 gtAaaAaggGGAaG.
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6761 1.30e+04 GCTGCaGc
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6826 6.80e+02 GGCAAaACcc
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6827 2.50e+03 GccTTC
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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 CAC0081

CAC0081 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Response regulator of the LytR/AlgR family cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC0081

CAC0081 has total of 55 gene neighbors in modules 53, 86
Gene neighbors (55)
Gene Common Name Description Module membership
CAC0012 CAC0012 Predicted dehydrogenase with iron-sulfur domain (NCBI ptt file) 86, 328
CAC0053 CAC0053 Hypothetical protein (NCBI ptt file) 70, 86
CAC0081 agrA Accessory gene regulator protein A (NCBI ptt file) 53, 86
CAC0199 CAC0199 Hypothetical protein (NCBI ptt file) 86, 244
CAC0309 CAC0309 Cell wall-associated hydrolase (NCBI ptt file) 4, 86
CAC0422 licT Transcriptional antiterminator licT (NCBI ptt file) 86, 328
CAC0437 CAC0437 Sensory transduction histidine kinase (NCBI ptt file) 53, 352
CAC0639 CAC0639 Flagellar biosynthesis related protein (NCBI ptt file) 53, 298
CAC0716 smpB TmRNA-binding protein SmpB (NCBI ptt file) 53, 304
CAC0761 CAC0761 Predicted membrane protein (NCBI ptt file) 66, 86
CAC0831 CAC0831 Sensory transduction histidine kinase (NCBI ptt file) 38, 53
CAC0910 CAC0910 Probably cellulosomal scaffolding protein precursor, secreted; cellulose-binding and cohesin domain (NCBI ptt file) 53, 63
CAC0912 CAC0912 Possible non-processive endoglucanase family 5, secreted; CelA homolog secreted; dockerin domain (NCBI ptt file) 53, 111
CAC0925 CAC0925 TPR-repeat-containing protein (NCBI ptt file) 53, 270
CAC1078 CAC1078 Predicted phosphohydrolase, Icc family (NCBI ptt file) 53, 267
CAC1169 CAC1169 Hypothetical protein (NCBI ptt file) 53, 134
CAC1170 xerD Integrase/recombinase (xerD/xerC family) (NCBI ptt file) 53, 267
CAC1199 CAC1199 Hypothetical protein (NCBI ptt file) 86, 123
CAC1228 cisA Site-specific DNA recombinase (NCBI ptt file) 26, 53
CAC1237 CAC1237 Hypothetical protein (NCBI ptt file) 86, 313
CAC1320 glpP Glycerol-3-phosphate responsive antiterminator (mRNA-binding), GLPP (NCBI ptt file) 4, 86
CAC1406 CAC1406 Transcriptional antiterminator (BglG family) (NCBI ptt file) 86, 133
CAC1452 CAC1452 MDR-type permease (NCBI ptt file) 26, 53
CAC1460 CAC1460 PTS system, fructose(mannose)-specific IID (NCBI ptt file) 86, 136
CAC1555 CAC1555 Flagellin (NCBI ptt file) 53, 69
CAC1770 CAC1770 RNA polymerase sigma factor, SigK-like (NCBI ptt file) 53, 68
CAC1772 sacB1 Levansucrase (NCBI ptt file) 53, 148
CAC1914 CAC1914 Hypothetical protein (NCBI ptt file) 11, 53
CAC1994 moaB Molybdopterin biosynthesis enzyme, MoaB (NCBI ptt file) 53, 68
CAC2013 CAC2013 Hypothetical protein (NCBI ptt file) 53, 97
CAC2015 CAC2015 Hypothetical protein (NCBI ptt file) 53, 97
CAC2079 CAC2079 Hypothetical protein (NCBI ptt file) 86, 272
CAC2133 CAC2133 Uncharacterized conserved protein, YLLB B.subtilis family (NCBI ptt file) 11, 53
CAC2291 CAC2291 Hypothetical protein (NCBI ptt file) 86, 102
CAC2331 CAC2331 DTDP-4-dehydrorhamnose 3,5-epimerase (NCBI ptt file) 86, 211
CAC2336 CAC2336 TPR repeats containing protein (NCBI ptt file) 53, 294
CAC2469 CAC2469 Lactoylglutathione lyase (fragment) (NCBI ptt file) 78, 86
CAC2494 CAC2494 Predicted membrane protein (NCBI ptt file) 53, 86
CAC2504 CAC2504 Hypothetical protein (NCBI ptt file) 4, 53
CAC2690 CAC2690 Transcriptional regulator, LysR family (NCBI ptt file) 86, 137
CAC2706 CAC2706 Uncharacterized conserved membrane protein, DedA family (NCBI ptt file) 53, 273
CAC2715 CAC2715 Hypothetical protein (NCBI ptt file) 26, 53
CAC2727 CAC2727 Predicted PHP family hydrolase (NCBI ptt file) 53, 278
CAC2826 CAC2826 Intracellular protease/amidase related enzyme (ThiJ family) (NCBI ptt file) 86, 273
CAC3033 CAC3033 Uncharacterized protein containing conserved domain, related to YABE B.subtilis C-terminal domain (NCBI ptt file) 86, 233
CAC3213 CAC3213 Possible stage V sporulation protein B, predicted transporter (NCBI ptt file) 86, 118
CAC3215 prsA Parvulin-like peptidyl-prolyl isomerase, PRSA B.subtilis ortholog (NCBI ptt file) 53, 59
CAC3226 CAC3226 Predicted membrane protein (NCBI ptt file) 86, 341
CAC3280 CAC3280 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 4, 86
CAC3286 CAC3286 Chey-like receiver domain containing protein, YCBB B.subtilis ortholog (NCBI ptt file) 86, 328
CAC3313 CAC3313 Acyl carrier protein, ACP (NCBI ptt file) 86, 341
CAC3359 CAC3359 Nitroreductase family protein fused to ferredoxin domain (NCBI ptt file) 86, 266
CAC3395 CAC3395 Predicted membrane protein (NCBI ptt file) 57, 86
CAC3535 CAC3535 Type II restriction enzyme, methylase subunit (NCBI ptt file) 53, 222
CAC3602 CAC3602 HD superfamily hydrolase (NCBI ptt file) 86, 109
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 CAC0081
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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