Organism : Clostridium acetobutylicum | Module List :
CAC0541

SAM-dependent methyltransferase (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Methylase involved in ubiquinone/menaquinone biosynthesis cog/ cog
metabolic process go/ biological_process
O-methyltransferase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0541
(Mouseover regulator name to see its description)

CAC0541 is regulated by 23 influences and regulates 0 modules.
Regulators for CAC0541 (23)
Regulator Module Operator
CAC0197 185 tf
CAC0465 185 tf
CAC0745 185 tf
CAC0860 185 tf
CAC1046 185 tf
CAC1800 185 tf
CAC2473 185 tf
CAC3349 185 tf
CAC3481 185 tf
CAC3509 185 tf
CAC3525 185 tf
CAC3687 185 tf
CAC0289 223 tf
CAC0599 223 tf
CAC1046 223 tf
CAC2074 223 tf
CAC2486 223 tf
CAC2568 223 tf
CAC2818 223 tf
CAC2889 223 tf
CAC3271 223 tf
CAC3472 223 tf
CAC3525 223 tf

Warning: CAC0541 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
7022 7.10e+03 CAGGCC
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7023 7.20e+01 gGAtTaTAagggggaGgcgT
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7098 5.70e+03 GGAcCG
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7099 5.30e+00 CacCTcta
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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 CAC0541

CAC0541 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Methylase involved in ubiquinone/menaquinone biosynthesis cog/ cog
metabolic process go/ biological_process
O-methyltransferase activity go/ molecular_function
Module neighborhood information for CAC0541

CAC0541 has total of 43 gene neighbors in modules 185, 223
Gene neighbors (43)
Gene Common Name Description Module membership
CAC0055 CAC0055 Uncharacterized predicted metal-binding protein, ortholog of Streptomyces (2808777) (NCBI ptt file) 71, 185
CAC0123 CAC0123 Cytosine deaminase (NCBI ptt file) 30, 223
CAC0160 CAC0160 Predicted acetyltransferase (NCBI ptt file) 185, 345
CAC0167 CAC0167 Possible sigma factor, diverged member of sigF/sigE/sigG family (NCBI ptt file) 191, 223
CAC0239 CAC0239 Histidine kinase-like ATPase (NCBI ptt file) 185, 346
CAC0417 CAC0417 Similar to arsenate reductase (NCBI ptt file) 71, 185
CAC0420 CAC0420 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 185, 247
CAC0463 CAC0463 Serine protease Do (heat-shock protein) (NCBI ptt file) 207, 223
CAC0541 CAC0541 SAM-dependent methyltransferase (NCBI ptt file) 185, 223
CAC0597 gerKB Spore germination protein, gerKB (NCBI ptt file) 115, 185
CAC0599 CAC0599 Transcriptional regulator, GntR family (NCBI ptt file) 223, 291
CAC0608 lisA Diaminopimelate decarboxilase, lisA (NCBI ptt file) 202, 223
CAC0720 CAC0720 Hypothetical protein (NCBI ptt file) 223, 240
CAC0747 CAC0747 Secreted protein containing uncharacterized conserved protein of ErfK family (NCBI ptt file) 49, 185
CAC0757 CAC0757 Predicted membrane protein (NCBI ptt file) 70, 223
CAC0851 CAC0851 Ortholog ygiD E.coli (NCBI ptt file) 167, 185
CAC0860 CAC0860 Two-component response regulator (NCBI ptt file) 185, 206
CAC1040 CAC1040 Predicted amidohydrolases (NCBI ptt file) 185, 346
CAC1083 CAC1083 Predicted membrane-associated metal-binding protein (NCBI ptt file) 185, 251
CAC1490 CAC1490 Hypothetical protein (NCBI ptt file) 185, 259
CAC1491 CAC1491 Predicted ATPase (NCBI ptt file) 146, 185
CAC1557 CAC1557 Predicted acetyltransferase (NCBI ptt file) 1, 185
CAC1581 CAC1581 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 185, 259
CAC1670 CAC1670 Response regulator (CheY-like receiver domain and DNA-binding HTH domain) (NCBI ptt file) 185, 326
CAC1970 CAC1970 Hypothetical protein (NCBI ptt file) 185, 326
CAC2546 CAC2546 Transcriptional regulator, FadR family (NCBI ptt file) 185, 276
CAC2557 CAC2557 Hypothetical protein (NCBI ptt file) 223, 349
CAC2568 CAC2568 Predicted transcriptional regulator (NCBI ptt file) 71, 223
CAC2759 CAC2759 Response regulator (CheY receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 71, 185
CAC2818 CAC2818 AraC-type DNA-binding domain-containing protein, transcriptional regulator (NCBI ptt file) 223, 241
CAC2930 CAC2930 Uncharacterized conserved membrane protein (NCBI ptt file) 71, 223
CAC2931 CAC2931 Uncharacterized conserved membrane protein (NCBI ptt file) 71, 223
CAC2932 CAC2932 ABC-type MDR transporter, ATPase component (NCBI ptt file) 223, 349
CAC3000 CAC3000 Hypothetical protein (NCBI ptt file) 92, 223
CAC3027 CAC3027 Predicted phosphohydrolase (NCBI ptt file) 216, 223
CAC3271 CAC3271 Transcriptional regulator, AcrR family (NCBI ptt file) 223, 285
CAC3321 CAC3321 Uncharacterized protein homolog of yveG B.subtilis (NCBI ptt file) 185, 216
CAC3381 CAC3381 Membrane protease subunit, stomatin/prohibitin homolog (NCBI ptt file) 15, 223
CAC3435 CAC3435 Hypothetical protein (NCBI ptt file) 185, 359
CAC3471 CAC3471 GMP reductase (NCBI ptt file) 223, 301
CAC3525 CAC3525 Uncharacterized conserved protein, YjeB/RRF2 family (NCBI ptt file) 223, 349
CAC3581 CAC3581 HAD superfamily hydrolase (NCBI ptt file) 185, 289
CAC3656 CAC3656 Uncharacterized conserved protein, yaiN/yohL family (NCBI ptt file) 185, 291
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 CAC0541
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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