Organism : Clostridium acetobutylicum | Module List :
CAC3088

NtrC family transcriptional regulator, ATPase domain fused to two PAS domains (NCBI ptt file)

CircVis
Functional Annotations (12)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
sugar:hydrogen symporter activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
phosphoenolpyruvate-dependent sugar phosphotransferase system go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3088
(Mouseover regulator name to see its description)

CAC3088 is regulated by 22 influences and regulates 5 modules.
Regulators for CAC3088 (22)
Regulator Module Operator
CAC0023 113 tf
CAC0144 113 tf
CAC0162 113 tf
CAC0841 113 tf
CAC1467 113 tf
CAC1670 113 tf
CAC1947 113 tf
CAC2052 113 tf
CAC2473 113 tf
CAC2851 113 tf
CAC3088 113 tf
CAC3360 113 tf
CAC3502 113 tf
CAC1046 287 tf
CAC1800 287 tf
CAC2473 287 tf
CAC2552 287 tf
CAC2568 287 tf
CAC3088 287 tf
CAC3507 287 tf
CAC3509 287 tf
CAC3611 287 tf

Warning: CAC3088 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
6878 8.20e-05 GgAgGaGa
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6879 8.70e+03 CcTcACGG
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7226 2.00e-02 .aGGtG
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7227 4.00e+04 cGTAATTcACATAAAaGGTc
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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 CAC3088

CAC3088 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
sugar:hydrogen symporter activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
phosphoenolpyruvate-dependent sugar phosphotransferase system go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
sensory_box tigr/ tigrfam
Module neighborhood information for CAC3088

CAC3088 has total of 45 gene neighbors in modules 113, 287
Gene neighbors (45)
Gene Common Name Description Module membership
CAC0011 CAC0011 Uncharacterized conserved of ErfK family (NCBI ptt file) 113, 279
CAC0237 CAC0237 ABC transporter, permease component (NCBI ptt file) 106, 287
CAC0246 CAC0246 Conserved membrane protein, predicted permease (NCBI ptt file) 66, 113
CAC0291 CAC0291 FUSION: methionine sintase I (cobalamin dependent) and 5,10 methylenetetrahydrofolate reductase (NCBI ptt file) 259, 287
CAC0366 CAC0366 Predicted permease (NCBI ptt file) 113, 282
CAC0371 CAC0371 Response regulator (CheY-like domain and HTH domain) (NCBI ptt file) 71, 287
CAC0375 patA PLP-dependent aminotransferase (gene patA) (NCBI ptt file) 99, 113
CAC0418 CAC0418 Predicted phosphatase, HAD family (NCBI ptt file) 261, 287
CAC0447 feoA FeoA protein, involved in Fe2+ transport (NCBI ptt file) 113, 227
CAC0605 CAC0605 Predicted phosphatase (NCBI ptt file) 287, 356
CAC0607 CAC0607 Aspartyl aminopeptidase (NCBI ptt file) 287, 309
CAC0906 CAC0906 Alanyl-tRNA synthetase related protein (NCBI ptt file) 113, 154
CAC0907 CAC0907 Uncharacterized conserved protein YjbQ/UPF0047 family, ortholog yugU B.subtilis (NCBI ptt file) 113, 227
CAC1018 CAC1018 Predicted membrane protein (NCBI ptt file) 287, 326
CAC1046 CAC1046 Transcriptional regulator, LysR family (NCBI ptt file) 71, 287
CAC1304 CAC1304 Uncharacterized conserved protein, predicted metal-binding (NCBI ptt file) 113, 363
CAC1330 CAC1330 Metal-dependent hydrolases of the beta-lactamase superfamily, possible sulfatase (NCBI ptt file) 287, 356
CAC1424 CAC1424 Zn-dependent hydrolase, glyoxylase II family (NCBI ptt file) 287, 326
CAC1438 CAC1438 Hypothetical protein (NCBI ptt file) 113, 158
CAC1443 CAC1443 Hypothetical protein (NCBI ptt file) 113, 181
CAC1480 CAC1480 Predicted dehydrogenase (NCBI ptt file) 113, 134
CAC1516 CAC1516 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 140, 287
CAC1582 CAC1582 Membrane associated histidine kinase-like ATPase (NCBI ptt file) 259, 287
CAC1591 CAC1591 Uncharacterized membrane protein, YCGQ B. subtilis homolog (NCBI ptt file) 113, 115
CAC1665 CAC1665 Predicted amidohydrolase (NCBI ptt file) 41, 113
CAC1666 CAC1666 Predicted membrane protein (NCBI ptt file) 113, 238
CAC1969 CAC1969 Possible plasmid transfer factor, TraK (NCBI ptt file) 287, 291
CAC1979 CAC1979 Predicted membrane protein (NCBI ptt file) 113, 363
CAC2472 CAC2472 Alpha/beta superfamily hydrolase (NCBI ptt file) 261, 287
CAC2486 CAC2486 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 113, 218
CAC2561 CAC2561 Predicted acetyltransferase (NCBI ptt file) 113, 210
CAC2625 CAC2625 Predicted membrane protein (NCBI ptt file) 41, 113
CAC2687 recQ RecQ protein, superfamily II DNA helicase (NCBI ptt file) 113, 345
CAC2735 CAC2735 Response regulator (CheY-like receiver domain and HTH-type DNA-binding) (NCBI ptt file) 74, 287
CAC2994 CAC2994 Toxic anion resistance protein, TELA family, YCEH B.subtilis ortholog (NCBI ptt file) 113, 146
CAC2996 CAC2996 Superfamily II DNA/RNA helicase, SNF2 family (NCBI ptt file) 259, 287
CAC3088 CAC3088 NtrC family transcriptional regulator, ATPase domain fused to two PAS domains (NCBI ptt file) 113, 287
CAC3243 CAC3243 Membrane associated methyl-accepting chemotaxis protein (NCBI ptt file) 113, 342
CAC3376 CAC3376 Possible pectin degradation protein (sugar phosphate isomerase family) (NCBI ptt file) 113, 292
CAC3457 CAC3457 Predicted membrane protein (NCBI ptt file) 287, 356
CAC3509 CAC3509 Transcriptional regulator, MerR family (duplicated domains) (NCBI ptt file) 287, 356
CAC3536 CAC3536 Uncharacterized conserved protein, YbeA family (NCBI ptt file) 113, 222
CAC3587 CAC3587 DNA replication protein DnaD (NCBI ptt file) 13, 287
CAC3695 CAC3695 Possible transcriptional regulator, containing DNA-binding domain of xre family (NCBI ptt file) 113, 292
CAC3696 CAC3696 Uncharacterized conserved membrane protein, YUEB B.subtilis homolog (NCBI ptt file) 113, 336
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 CAC3088
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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