Organism : Clostridium acetobutylicum | Module List :
CAC0265

Transcriptional regulator, GntR family (NCBI ptt file)

CircVis
Functional Annotations (4)
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
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0265
(Mouseover regulator name to see its description)

CAC0265 is regulated by 24 influences and regulates 35 modules.
Regulators for CAC0265 (24)
Regulator Module Operator
CAC0265 77 tf
CAC0876 77 tf
CAC1333 77 tf
CAC1430 77 tf
CAC1469 77 tf
CAC1668 77 tf
CAC1832 77 tf
CAC1950 77 tf
CAC2773 77 tf
CAC3338 77 tf
CAC3481 77 tf
CAC3553 77 tf
CAC0032 147 tf
CAC0197 147 tf
CAC0265 147 tf
CAC0763 147 tf
CAC0876 147 tf
CAC0929 147 tf
CAC1668 147 tf
CAC1696 147 tf
CAC2773 147 tf
CAC2793 147 tf
CAC2934 147 tf
CAC3063 147 tf

Warning: CAC0265 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
6808 8.50e-04 agGaGGtaaaT
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6809 2.80e+04 CaCcTATCTcTcC
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6946 5.50e-05 GgaGGa
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6947 2.70e+02 cGccTTACCAACACaGGC
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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 CAC0265

CAC0265 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
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
Module neighborhood information for CAC0265

CAC0265 has total of 33 gene neighbors in modules 77, 147
Gene neighbors (33)
Gene Common Name Description Module membership
CAC0129 bofA BofA B.subtilis ortholog, SigmaK-factor processing regulatory protein (NCBI ptt file) 77, 304
CAC0197 CAC0197 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 27, 147
CAC0264 CAC0264 Predicted membrane protein (NCBI ptt file) 77, 147
CAC0265 CAC0265 Transcriptional regulator, GntR family (NCBI ptt file) 77, 147
CAC0266 CAC0266 ABC transporter, ATP-binding protein (NCBI ptt file) 77, 147
CAC0323 CAC0323 Sensory transduction histidine kinase (NCBI ptt file) 99, 147
CAC0331 CAC0331 Uncharacterized membrane protein, homolog of YPAA B.subtilis (NCBI ptt file) 147, 231
CAC0390 CAC0390 Cystathionine gamma-synthase (NCBI ptt file) 147, 167
CAC0391 CAC0391 Cystathionine beta-lyase (NCBI ptt file) 147, 167
CAC0850 CAC0850 Nitroreductase family protein (NCBI ptt file) 77, 167
CAC0872 CAC0872 Xanthine permease (NCBI ptt file) 77, 303
CAC0876 CAC0876 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 77, 348
CAC0877 cfa Cyclopropane fatty acid synthase (NCBI ptt file) 77, 348
CAC0878 CAC0878 Amino acid ABC transporter permease component (NCBI ptt file) 147, 303
CAC0879 CAC0879 ABC-type polar amino acid transport system, ATPase component (NCBI ptt file) 147, 303
CAC0880 CAC0880 Periplasmic amino acid binding protein (NCBI ptt file) 23, 147
CAC1006 CAC1006 MutT-like (Nudix) hydrolase (NCBI ptt file) 77, 167
CAC1038 CAC1038 Predicted metal-binding membrane protein (NCBI ptt file) 77, 179
CAC1041 argS Arginyl-tRNA synthetase (NCBI ptt file) 147, 296
CAC1353 CAC1353 Phosphotransferase system IIC component, possibly N-acetylglucosamine-specific (NCBI ptt file) 147, 237
CAC1584 CAC1584 Metal-dependent hydrolase of the beta-lactamase superfamily (NCBI ptt file) 77, 322
CAC1832 lexA SOS regulatory protein LexA (NCBI ptt file) 77, 162
CAC2367 CAC2367 Uncharacterized protein containing predicted cell adhesion domain and ChW-repeats (NCBI ptt file) 77, 296
CAC2558 CAC2558 Hypothetical protein (NCBI ptt file) 147, 216
CAC2613 glcK Transcriptional regulators of NagC/XylR family (NCBI ptt file) 11, 147
CAC2772 CAC2772 Permease (NCBI ptt file) 77, 262
CAC2943 CAC2943 N-terminal domain intergin-like repeats and c-terminal - cell wall-associated hydrolase domain (NCBI ptt file) 77, 262
CAC2995 CAC2995 PTS system (Glucose-specific) component IIA (NCBI ptt file) 77, 179
CAC3013 CAC3013 Hypothetical protein (NCBI ptt file) 77, 147
CAC3295 CAC3295 Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file) 77, 348
CAC3297 CAC3297 D-alanyl-D-alanine carboxypeptidase family hydrolase, YODJ B.subtilis ortholog (NCBI ptt file) 147, 262
CAC3362 CAC3362 Uncharacterized conserved membrane protein, YOAK B.subtilis homolog (NCBI ptt file) 52, 147
CAC3664 CAC3664 Predicted flavodoxin (NCBI ptt file) 23, 147
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 CAC0265
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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