Organism : Clostridium acetobutylicum | Module List :
CAC3443 bltR

Multidrug-efflux transporter transcription regulator, BltR (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator, effector-binding domain/component cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3443
(Mouseover regulator name to see its description)

CAC3443 is regulated by 23 influences and regulates 10 modules.
Regulators for CAC3443 bltR (23)
Regulator Module Operator
CAC0289 28 tf
CAC0445 28 tf
CAC0571 28 tf
CAC0951 28 tf
CAC1451 28 tf
CAC2071 28 tf
CAC2306 28 tf
CAC3199 28 tf
CAC3443 28 tf
CAC0289 202 tf
CAC1264 202 tf
CAC1467 202 tf
CAC1481 202 tf
CAC1869 202 tf
CAC1928 202 tf
CAC2236 202 tf
CAC2768 202 tf
CAC3370 202 tf
CAC3443 202 tf
CAC3472 202 tf
CAC3488 202 tf
CAC3646 202 tf
CAC3677 202 tf

Warning: CAC3443 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
6710 1.40e-02 CCTCctta
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6711 3.30e+03 CccAGcaGG
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7056 8.20e+00 GaaAgGAGGat
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7057 4.00e+02 GtGGaGtgc
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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 CAC3443

CAC3443 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulator, effector-binding domain/component cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC3443

CAC3443 has total of 35 gene neighbors in modules 28, 202
Gene neighbors (35)
Gene Common Name Description Module membership
CAC0066 CAC0066 ABC transporter, ATP-binding protein (NCBI ptt file) 28, 353
CAC0119 cheW Chemotaxis protein cheW (NCBI ptt file) 19, 28
CAC0169 CAC0169 ABC transporter (ATP-binding protein) (NCBI ptt file) 169, 202
CAC0170 CAC0170 Predicted permease (NCBI ptt file) 169, 202
CAC0171 CAC0171 Predicted permease (NCBI ptt file) 169, 202
CAC0339 CAC0339 ADP-ribosylglycohydrolase (NCBI ptt file) 148, 202
CAC0383 CAC0383 PTS cellobiose-specific component IIA (NCBI ptt file) 28, 324
CAC0529 CAC0529 Acetylxylan esterase related enzyme (NCBI ptt file) 202, 327
CAC0608 lisA Diaminopimelate decarboxilase, lisA (NCBI ptt file) 202, 223
CAC0736 CAC0736 Possible glucanotransferase (putative endo alpha-1,4 polygalactosaminidase related protein) (NCBI ptt file) 28, 241
CAC0773 CAC0773 ABC-type cobalt transport protein ATPase component (NCBI ptt file) 28, 253
CAC0797 CAC0797 Phosphoenolpyruvate synthase (NCBI ptt file) 202, 212
CAC0798 CAC0798 Phosphatidylserine synthase (NCBI ptt file) 28, 202
CAC0818 CAC0818 Diguanylate cyclase/phosphodiesterase domain (GGDEF) containing protein (NCBI ptt file) 183, 202
CAC0828 CAC0828 Hypothetical protein (NCBI ptt file) 145, 202
CAC1021 CAC1021 Predicted Fe-S oxidoreductases (NCBI ptt file) 28, 105
CAC1088 glpX GlpX-like protein (Fructose-1,6-bisphosphatase related protein) (NCBI ptt file) 19, 28
CAC1327 CAC1327 Hypothetical protein (NCBI ptt file) 165, 202
CAC1435 CAC1435 S-adenosylmethionine-dependent methyltransferases (NCBI ptt file) 28, 327
CAC1574 CAC1574 NAD-dependent 4-hydroxybutyrate dehydrogenase (NCBI ptt file) 28, 90
CAC2172 CAC2172 Predicted glycosyltransferase (NCBI ptt file) 28, 96
CAC2246 CAC2246 Lysophospholipase L2 PLDB, hydrolase of alpha/beta superfamily (NCBI ptt file) 28, 79
CAC2290 nprE Extracellular neutral metalloprotease, NPRE, fused to ChW-repeats (NCBI ptt file) 161, 202
CAC2401 CAC2401 Activator of 2-hydroxyglutaryl-CoA dehydratase (duplicated HSP70 class ATPase domain) fused to uncharacterized conserved protein (NCBI ptt file) 28, 84
CAC2455 CAC2455 Hypothetical protein, CF-13 family (NCBI ptt file) 202, 240
CAC2532 CAC2532 Protein containing ChW-repeats (NCBI ptt file) 144, 202
CAC2548 CAC2548 Reductase/isomerase/elongation factor common domain (NCBI ptt file) 94, 202
CAC2813 CAC2813 Predicted integrase of XerC/XerD family (NCBI ptt file) 202, 338
CAC2879 upp Uracil phosphoribosyltransferase (NCBI ptt file) 28, 310
CAC2935 CAC2935 Predicted acetyltransferase (NCBI ptt file) 120, 202
CAC3323 CAC3323 Predicted membrane protein (NCBI ptt file) 165, 202
CAC3441 CAC3441 DNA/RNA helicase, SNF2 (NCBI ptt file) 28, 353
CAC3442 polC DNA polymerase III (alpha subunit) (NCBI ptt file) 28, 353
CAC3443 bltR Multidrug-efflux transporter transcription regulator, BltR (NCBI ptt file) 28, 202
CAC3663 CAC3663 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 202, 240
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 CAC3443
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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