Organism : Clostridium acetobutylicum | Module List :
CAC2851

GntR/FadR-family transcriptional regulator fused to conserved membrane protein (YHCF B.subtilis homolog) (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
potassium ion transport go/ biological_process
cation transmembrane transporter activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2851
(Mouseover regulator name to see its description)

CAC2851 is regulated by 22 influences and regulates 9 modules.
Regulators for CAC2851 (22)
Regulator Module Operator
CAC0144 149 tf
CAC0255 149 tf
CAC0284 149 tf
CAC0569 149 tf
CAC0766 149 tf
CAC1333 149 tf
CAC1569 149 tf
CAC2430 149 tf
CAC2851 149 tf
CAC3475 149 tf
CAC0255 60 tf
CAC0289 60 tf
CAC0863 60 tf
CAC0933 60 tf
CAC1698 60 tf
CAC2794 60 tf
CAC2851 60 tf
CAC3267 60 tf
CAC3424 60 tf
CAC3606 60 tf
CAC3646 60 tf
CAC3649 60 tf

Warning: CAC2851 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
6774 3.30e+01 GGgGGA
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6775 9.20e+02 gAGGtgAG
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6950 4.60e-03 AGgagggA
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6951 2.20e+03 GAGaGGTAcCaCG
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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 CAC2851

CAC2851 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
potassium ion transport go/ biological_process
cation transmembrane transporter activity go/ molecular_function
Module neighborhood information for CAC2851

CAC2851 has total of 37 gene neighbors in modules 60, 149
Gene neighbors (37)
Gene Common Name Description Module membership
CAC0085 CAC0085 Hypothetical protein (NCBI ptt file) 60, 99
CAC0190 CAC0190 Beta-lactamase (NCBI ptt file) 60, 155
CAC0569 sacT SACPA operon antiterminator (sacT) (NCBI ptt file) 149, 277
CAC0647 CAC0647 Predicted membrane protein (NCBI ptt file) 149, 344
CAC0648 CAC0648 Molecular chaperone, DnaJ family (contain C-term. Zn finger domain) (NCBI ptt file) 149, 346
CAC0676 pssA Phosphatidylserine synthase (NCBI ptt file) 149, 282
CAC0853 CAC0853 HD superfamily hydrolase (HD-GYP domain) (NCBI ptt file) 60, 248
CAC1042 CAC1042 Predicted membrane protein (NCBI ptt file) 149, 296
CAC1333 CAC1333 AraC-type sugar metabolism regulator (NCBI ptt file) 149, 252
CAC1506 phoP Response regulator (CheY-like receiver domain and a HTH) (NCBI ptt file) 140, 149
CAC1569 CAC1569 Transcriptional regulators, MarR/EmrR family (NCBI ptt file) 149, 252
CAC1612 CAC1612 Probable cation efflux pump, multidrug resistance protein (FS) (NCBI ptt file) 76, 149
CAC1768 CAC1768 Uncharacterized conserved protein, TraB family (NCBI ptt file) 60, 155
CAC2004 CAC2004 Siderophore/Surfactin synthetase related protein (NCBI ptt file) 60, 209
CAC2023 CAC2023 Membrane protein, related to copy number protein COP from Clostridium perfringens plasmid pIP404 (GI:116928) (NCBI ptt file) 60, 149
CAC2041 CAC2041 ABC transported MDR-type, permease component (NCBI ptt file) 60, 293
CAC2042 CAC2042 ABC transported MDR-type, permease component (NCBI ptt file) 60, 155
CAC2258 CAC2258 Hypothetical protein (NCBI ptt file) 149, 252
CAC2277 secF Preprotein translocase subunit SecF (NCBI ptt file) 8, 149
CAC2289 CAC2289 Biotin carboxyl carrier protein (NCBI ptt file) 60, 155
CAC2430 greA Transcription elongation factor, greA (NCBI ptt file) 149, 252
CAC2478 CAC2478 Predicted conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 13, 149
CAC2514 CAC2514 Beta galactosidase (NCBI ptt file) 60, 155
CAC2515 CAC2515 Hypothetical protein (NCBI ptt file) 149, 341
CAC2555 CAC2555 Hypothetical protein (NCBI ptt file) 13, 149
CAC2597 CAC2597 Hypothetical protein (NCBI ptt file) 60, 267
CAC2662 CAC2662 Hypothetical protein (NCBI ptt file) 60, 115
CAC2693 CAC2693 Predicted membrane protein (NCBI ptt file) 27, 60
CAC2695 CAC2695 Diverged Metallo-dependent hydrolase(Zn) of DD-Peptidase family; peptodoglycan-binding domain (NCBI ptt file) 60, 178
CAC2851 CAC2851 GntR/FadR-family transcriptional regulator fused to conserved membrane protein (YHCF B.subtilis homolog) (NCBI ptt file) 60, 149
CAC2852 comFC Predicted amidophosphoribosyltransferase, ComFC B.suntilis ortholog (NCBI ptt file) 76, 149
CAC2853 CAC2853 Hypothetical protein (NCBI ptt file) 25, 149
CAC2940 CAC2940 Membrane-associated sensory histidine kinase-like ATPase (NCBI ptt file) 149, 252
CAC3193 CAC3193 Hypothetical protein (NCBI ptt file) 130, 149
CAC3411 CAC3411 Homolog of plant auxin-responsive GH3-like protein (NCBI ptt file) 60, 155
CAC3460 CAC3460 Hypothetical protein, CF-28 family (NCBI ptt file) 60, 99
CAC3646 CAC3646 Predicted transcriptional regulator, containing DNA-binding domain of xre family (NCBI ptt file) 60, 269
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 CAC2851
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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