Organism : Clostridium acetobutylicum | Module List :
CAC0093

Transcriptional regulators, LysR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0093
(Mouseover regulator name to see its description)

CAC0093 is regulated by 21 influences and regulates 8 modules.
Regulators for CAC0093 (21)
Regulator Module Operator
CAC0197 216 tf
CAC0265 216 tf
CAC0465 216 tf
CAC0723 216 tf
CAC0849 216 tf
CAC2842 216 tf
CAC3088 216 tf
CAC3216 216 tf
CAC3481 216 tf
CAC3606 216 tf
CAC0093 301 tf
CAC1280 301 tf
CAC1467 301 tf
CAC1867 301 tf
CAC2306 301 tf
CAC2605 301 tf
CAC2955 301 tf
CAC3271 301 tf
CAC3466 301 tf
CAC3651 301 tf
CAC3677 301 tf

Warning: CAC0093 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
7084 3.30e+01 gAGGaggtt
Loader icon
7085 6.10e+00 CCtCCc
Loader icon
7254 1.30e+00 AAaacagGagGggt
Loader icon
7255 3.40e+04 GTccACG
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 CAC0093

CAC0093 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC0093

CAC0093 has total of 46 gene neighbors in modules 216, 301
Gene neighbors (46)
Gene Common Name Description Module membership
CAC0093 CAC0093 Transcriptional regulators, LysR family (NCBI ptt file) 216, 301
CAC0154 MtlA PTS system, mannitol-specific IIBC component (gene MtlA) (NCBI ptt file) 301, 342
CAC0332 manB Beta-mannanase (NCBI ptt file) 191, 301
CAC0372 CAC0372 Sensory transduction histidine kinase (HisKA and HATPase damains) (NCBI ptt file) 216, 224
CAC0388 CAC0388 Hypothetical protein (NCBI ptt file) 301, 361
CAC0534 pps Phosphoenolpyruvate synthase (gene pps) (NCBI ptt file) 65, 301
CAC0577 CAC0577 Endo-arabinase related enzyme (family 43 glycosyl hydrolase domain and ricin B-like domain) (NCBI ptt file) 150, 216
CAC0690 CAC0690 Endoglucanase, aminopeptidase M42 family (NCBI ptt file) 216, 238
CAC0695 CAC0695 Altronate oxidoreductase (NCBI ptt file) 170, 301
CAC0849 CAC0849 Predicted transcriptional regulator (NCBI ptt file) 151, 216
CAC0858 CAC0858 Phosphinothricin acetyltransferase (NCBI ptt file) 71, 216
CAC1140 CAC1140 Hypothetical protein (NCBI ptt file) 16, 301
CAC1444 CAC1444 Uncharacterized conserved membrane protein, similar to MDR (VANZ) ORF of Enterococcus (NCBI ptt file) 132, 216
CAC1477 CAC1477 Hypothetical protein (NCBI ptt file) 272, 301
CAC1497 CAC1497 Uncharacterized protein, homolog of YCGL B.subtilis (NCBI ptt file) 216, 240
CAC1526 CAC1526 Amidase, related to GSP of E.coli (NCBI ptt file) 26, 301
CAC1676 CAC1676 Uncharacterized conserved protein (NCBI ptt file) 301, 332
CAC1867 CAC1867 Transcriptional regulator (phage-related) (Xre family) (NCBI ptt file) 301, 342
CAC2244 CAC2244 HAD superfamily hydrolases, YKRA B.subtilis ortholog (NCBI ptt file) 216, 251
CAC2247 CAC2247 Site-specific recombinase, DNA invertase Pin homolog (NCBI ptt file) 270, 301
CAC2509 CAC2509 Predicted acetyltransferase (NCBI ptt file) 165, 301
CAC2521 CAC2521 Hypothetical protein, CF-41 family (NCBI ptt file) 94, 216
CAC2540 CAC2540 Co/Zn/Cd efflux system component (NCBI ptt file) 207, 301
CAC2558 CAC2558 Hypothetical protein (NCBI ptt file) 147, 216
CAC2600 CAC2600 Predicted membrane protein (NCBI ptt file) 300, 301
CAC2689 CAC2689 Uncharacterized protein, YJCM B.subtilis ortholog (NCBI ptt file) 4, 216
CAC2760 CAC2760 Membrane-associated sensory histidine kinase with HAMP domain (NCBI ptt file) 132, 216
CAC2822 CAC2822 TPR-repeat-containing protein (NCBI ptt file) 165, 301
CAC2837 CAC2837 Fusion HD-GYP domain and HD-hydrolase domain (NCBI ptt file) 212, 216
CAC3024 CAC3024 acyl-CoA thioesterase family protein (NCBI ptt file) 216, 309
CAC3027 CAC3027 Predicted phosphohydrolase (NCBI ptt file) 216, 223
CAC3164 CAC3164 Lysine-specific permease (NCBI ptt file) 265, 301
CAC3237 msmX Multiple sugar-binding ABC-transporter, MSMX ATP-binding protein (NCBI ptt file) 301, 312
CAC3241 CAC3241 Uncharacterized conserved membrane protein, YYAD B.subtilis ortholog (NCBI ptt file) 150, 301
CAC3242 CAC3242 Uncharacterized Fe-S protein, PflX (pyruvate formate lyase activating protein) homolog (NCBI ptt file) 72, 301
CAC3321 CAC3321 Uncharacterized protein homolog of yveG B.subtilis (NCBI ptt file) 185, 216
CAC3371 CAC3371 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase domains) (NCBI ptt file) 122, 216
CAC3451 CAC3451 Sugar/Na+(H+) simporter (NCBI ptt file) 170, 301
CAC3468 uvrC Excinuclease ABC, subunit C (uvrC) (NCBI ptt file) 207, 301
CAC3471 CAC3471 GMP reductase (NCBI ptt file) 223, 301
CAC3484 CAC3484 Short-chain alcohol dehydrogenase family protein (NCBI ptt file) 206, 216
CAC3490 CAC3490 DNA gyrase inhibitory protein, GyrI (NCBI ptt file) 205, 301
CAC3590 CAC3590 Predicted flavoprotein, YhiN family (NCBI ptt file) 174, 301
CAC3606 CAC3606 Transcriptional regulator, AcrR family (NCBI ptt file) 74, 216
CAC3607 CAC3607 Possible ketopantoate reductase PanE/ApbA (NCBI ptt file) 83, 216
CAC3644 CAC3644 Oligopeptide ABC transporter, permease component (NCBI ptt file) 217, 301
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 CAC0093
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