Organism : Clostridium acetobutylicum | Module List :
CAC2451

SoxR family transcriptional regulator fused to SAM-dependent methyltransferase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Methylase involved in ubiquinone/menaquinone biosynthesis 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
methyltransferase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2451
(Mouseover regulator name to see its description)

CAC2451 is regulated by 22 influences and regulates 1 modules.
Regulators for CAC2451 (22)
Regulator Module Operator
CAC0019 341 tf
CAC1569 341 tf
CAC2394 341 tf
CAC2476 341 tf
CAC2616 341 tf
CAC3647 341 tf
CAC3695 341 tf
CAC0019 162 tf
CAC0155 162 tf
CAC0284 162 tf
CAC0379 162 tf
CAC0977 162 tf
CAC1569 162 tf
CAC1698 162 tf
CAC1832 162 tf
CAC2071 162 tf
CAC2476 162 tf
CAC2546 162 tf
CAC3200 162 tf
CAC3338 162 tf
CAC3553 162 tf
CAC3731 162 tf

Warning: CAC2451 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
6976 3.60e+03 CGGGcaGtG
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6977 7.90e+01 GgAGaaggT
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7334 8.10e-05 aGGAGG
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7335 7.20e+03 GGGCaaGGTc
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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 CAC2451

CAC2451 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Methylase involved in ubiquinone/menaquinone biosynthesis 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
methyltransferase activity go/ molecular_function
Module neighborhood information for CAC2451

CAC2451 has total of 43 gene neighbors in modules 162, 341
Gene neighbors (43)
Gene Common Name Description Module membership
CAC0019 CAC0019 Transcriptional regulator, AcrR family (NCBI ptt file) 73, 341
CAC0130 CAC0130 Uncharacterized membrane protein, YTAF B.subtilis ortholog (NCBI ptt file) 176, 341
CAC0142 CAC0142 Hypothetical protein (NCBI ptt file) 188, 341
CAC0292 CAC0292 Hypothetical protein (NCBI ptt file) 162, 276
CAC0523 CAC0523 SAM-dependent methyltransferase related to tRNA(uracyl-5-)-methyltransferase (trmA family) (NCBI ptt file) 254, 341
CAC0616 CAC0616 Predicted membrane protein (NCBI ptt file) 8, 162
CAC0686 CAC0686 Spore cortex-lytic enzyme prepeptide; peptodoglycan-binding domain (NCBI ptt file) 118, 341
CAC0844 CAC0844 Barstar-like protein ribonuclease (barnase) inhibitor (NCBI ptt file) 67, 341
CAC0967 CAC0967 Probably membrane protein (NCBI ptt file) 162, 233
CAC0997 ndk Probable nucleoside-diphosphate kinase N-terminal domain (NCBI ptt file) 11, 162
CAC1354 CAC1354 Phosphotransferase system IIA component (NCBI ptt file) 254, 341
CAC1388 manC Mannose-6-phosphate isomerase (NCBI ptt file) 162, 341
CAC1523 CAC1523 Fructokinase (NCBI ptt file) 162, 302
CAC1568 CAC1568 Diguanylate cyclase/phosphodiesterase domain 1 (GGDEF) (NCBI ptt file) 134, 162
CAC1641 CAC1641 Ankyrin repeats containing protein (NCBI ptt file) 162, 244
CAC1832 lexA SOS regulatory protein LexA (NCBI ptt file) 77, 162
CAC1873 CAC1873 Hypothetical protein (NCBI ptt file) 99, 162
CAC2070 CAC2070 Hypothetical protein (NCBI ptt file) 31, 162
CAC2417 CAC2417 Hypothetical protein (NCBI ptt file) 152, 162
CAC2451 CAC2451 SoxR family transcriptional regulator fused to SAM-dependent methyltransferase (NCBI ptt file) 162, 341
CAC2466 CAC2466 Predicted aldoketomutase of glyoxalase I family (NCBI ptt file) 162, 322
CAC2487 CAC2487 Predicted acetyltransferase (NCBI ptt file) 130, 162
CAC2500 CAC2500 Uncharacterized conserved membrane protein, YgiH/UPF0078 family (NCBI ptt file) 130, 162
CAC2502 CAC2502 Predicted permease (NCBI ptt file) 130, 341
CAC2515 CAC2515 Hypothetical protein (NCBI ptt file) 149, 341
CAC2602 CAC2602 Spermidine synthase (NCBI ptt file) 110, 341
CAC2659 CAC2659 Putative stress-responsive transcriptional regulator PspC (NCBI ptt file) 31, 162
CAC2823 CAC2823 Hypothetical protein (NCBI ptt file) 258, 341
CAC2872 CAC2872 Predicted membrane protein in FoF1-type ATP synthase operon (NCBI ptt file) 76, 162
CAC2982 CAC2982 MinD family ATPase (chromosome partitioning) (NCBI ptt file) 254, 341
CAC3005 add Adenosine deaminase (NCBI ptt file) 40, 341
CAC3226 CAC3226 Predicted membrane protein (NCBI ptt file) 86, 341
CAC3256 CAC3256 Predicted acetyltransferase (NCBI ptt file) 123, 341
CAC3264 CAC3264 Uncharacterized conserved protein, YTFJ B.subtilis ortholog (NCBI ptt file) 4, 341
CAC3313 CAC3313 Acyl carrier protein, ACP (NCBI ptt file) 86, 341
CAC3341 CAC3341 Multimeric flavodoxin WrbA family protein (NCBI ptt file) 4, 341
CAC3374 CAC3374 Predicted acetyltransferase (NCBI ptt file) 140, 162
CAC3450 CAC3450 Hypothetical protein (NCBI ptt file) 119, 341
CAC3491 CAC3491 Protein, related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) (NCBI ptt file) 312, 341
CAC3496 CAC3496 Predicted transcriptional regulator (NCBI ptt file) 179, 341
CAC3528 CAC3528 Hypothetical protein (NCBI ptt file) 130, 162
CAC3700 CAC3700 Hypothetical protein, CF-44 family (NCBI ptt file) 162, 304
CAC3701 CAC3701 Hypothetical protein, CF-44 family (NCBI ptt file) 162, 167
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 CAC2451
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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