Organism : Clostridium acetobutylicum | Module List :
CAC0078 agrB

Accessory gene regulator protein B (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Membrane protein putatively involved in post-translational modification of the autoinducing quorum-sensing peptide cog/ cog
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0078
(Mouseover regulator name to see its description)

CAC0078 is regulated by 15 influences and regulates 23 modules.
Regulators for CAC0078 agrB (15)
Regulator Module Operator
CAC0078 7 tf
CAC0191 7 tf
CAC0445 7 tf
CAC1467 7 tf
CAC2071 7 tf
CAC2084 7 tf
CAC2306 7 tf
CAC2307 7 tf
CAC3409 7 tf
CAC0078 178 tf
CAC0289 178 tf
CAC1467 178 tf
CAC2306 178 tf
CAC3409 178 tf
CAC3729 178 tf
Regulated by CAC0078 (23)
Module Residual Genes
7 0.27 14
18 0.22 13
90 0.37 19
92 0.44 27
94 0.32 15
96 0.27 14
107 0.31 15
153 0.36 20
155 0.29 16
178 0.27 14
191 0.42 24
200 0.30 17
212 0.36 19
217 0.36 19
219 0.33 19
228 0.31 16
248 0.30 15
285 0.33 19
289 0.41 20
291 0.34 23
292 0.41 24
325 0.29 16
360 0.45 24
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
6668 1.70e+02 GaGgTgaG
Loader icon
6669 6.40e+03 GTgGtAtAATT
Loader icon
7008 8.70e-02 AGGgGg
Loader icon
7009 8.90e+01 aca.CatTttAcAtt.atTgcg
Loader icon
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 CAC0078

CAC0078 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Membrane protein putatively involved in post-translational modification of the autoinducing quorum-sensing peptide cog/ cog
membrane go/ cellular_component
Module neighborhood information for CAC0078

CAC0078 has total of 23 gene neighbors in modules 7, 178
Gene neighbors (23)
Gene Common Name Description Module membership
CAC0078 agrB Accessory gene regulator protein B (NCBI ptt file) 7, 178
CAC0082 CAC0082 Predicted membrane protein (NCBI ptt file) 178, 292
CAC0193 CAC0193 Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file) 7, 174
CAC0194 CAC0194 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 7, 174
CAC0555 CAC0555 Predicted membrane protein (NCBI ptt file) 7, 134
CAC0792 CAC0792 D-amino acid aminotransferase (NCBI ptt file) 7, 178
CAC1010 CAC1010 Predicted phosphohydrolase, Icc family (NCBI ptt file) 155, 178
CAC1314 CAC1314 Hypothetical protein (NCBI ptt file) 18, 178
CAC1315 CAC1315 Peptodoglycan-binding domain containing protein (NCBI ptt file) 18, 178
CAC1467 CAC1467 Transcriptional regulator, Lrp family (NCBI ptt file) 178, 278
CAC2382 ssb Single-strand DNA-binding protein, ssb (NCBI ptt file) 18, 178
CAC2407 CAC2407 CheY-like receiver domain of response regulator (NCBI ptt file) 7, 155
CAC2408 CAC2408 Glycosyltransferase (NCBI ptt file) 7, 155
CAC2528 CAC2528 Multimeric flavodoxin WrbA fused to cytochrome c-like domain (NCBI ptt file) 7, 24
CAC2531 CAC2531 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 7, 200
CAC2581 CAC2581 6-pyruvoyl-tetrahydropterin synthase related domain; conserved membrane protein (NCBI ptt file) 18, 178
CAC2695 CAC2695 Diverged Metallo-dependent hydrolase(Zn) of DD-Peptidase family; peptodoglycan-binding domain (NCBI ptt file) 60, 178
CAC2722 CAC2722 RCC1 repeats protein (beta propeller fold) (NCBI ptt file) 7, 200
CAC3355 CAC3355 Polyketide synthase pksE (short-chain alcohol dehydrogenase,acyl-carrier-protein S-malonyltransferase,3-oxoacyl-(acyl-carrier-protein) synthase I domains) (NCBI ptt file) 7, 178
CAC3408 CAC3408 NADH oxidase (two distinct flavin oxidoreductase domains) (NCBI ptt file) 7, 178
CAC3409 alsR Transcriptional regulators, LysR family (NCBI ptt file) 7, 178
CAC3423 CAC3423 Acetyltransferase (ribosomal protein N-acetylase subfamily) (NCBI ptt file) 18, 178
CAC3558 CAC3558 Probable S-layer protein (NCBI ptt file) 7, 18
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 CAC0078
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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