Organism : Clostridium acetobutylicum | Module List :
CAC0584

Precorrin-6B methylase 1 CobL1/CbiE (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Precorrin-6B methylase 1 cog/ cog
protein methyltransferase activity go/ molecular_function
cobalamin biosynthetic process go/ biological_process
precorrin-6Y C5,15-methyltransferase (decarboxylating) activity go/ molecular_function
CbiE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0584
(Mouseover regulator name to see its description)

CAC0584 is regulated by 20 influences and regulates 0 modules.
Regulators for CAC0584 (20)
Regulator Module Operator
CAC0144 106 tf
CAC0841 106 tf
CAC1559 106 tf
CAC1766 106 tf
CAC2052 106 tf
CAC2060 106 tf
CAC2084 106 tf
CAC3192 106 tf
CAC3216 106 tf
CAC3267 106 tf
CAC3345 106 tf
CAC3409 106 tf
CAC0859 117 tf
CAC1340 117 tf
CAC1578 117 tf
CAC1950 117 tf
CAC2608 117 tf
CAC3152 117 tf
CAC3507 117 tf
CAC3611 117 tf

Warning: CAC0584 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
6864 4.40e-02 GgAGGg.T
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6865 6.50e+03 CGAGGTG
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6886 1.10e+02 gCtTCggcTt
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6887 1.40e+00 AGGaGg
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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 CAC0584

CAC0584 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Precorrin-6B methylase 1 cog/ cog
protein methyltransferase activity go/ molecular_function
cobalamin biosynthetic process go/ biological_process
precorrin-6Y C5,15-methyltransferase (decarboxylating) activity go/ molecular_function
CbiE tigr/ tigrfam
Module neighborhood information for CAC0584

CAC0584 has total of 44 gene neighbors in modules 106, 117
Gene neighbors (44)
Gene Common Name Description Module membership
CAC0111 CAC0111 Glutamine-binding periplasmic protein fused to glutamine permease (NCBI ptt file) 106, 278
CAC0112 glnQ Glutamine ABC transporter (ATP-binding protein) (NCBI ptt file) 106, 302
CAC0148 CAC0148 Predicted enzyme with TIM-barrel fold (NCBI ptt file) 117, 345
CAC0237 CAC0237 ABC transporter, permease component (NCBI ptt file) 106, 287
CAC0248 CAC0248 Transposon related protein (NCBI ptt file) 13, 117
CAC0325 CAC0325 Uncharacterized membrane protein, homolog of YtaF B.subtilis (NCBI ptt file) 13, 117
CAC0583 CAC0583 CBIK protein (chain A, anaerobic cobalt chelatase) (NCBI ptt file) 117, 344
CAC0584 CAC0584 Precorrin-6B methylase 1 CobL1/CbiE (NCBI ptt file) 106, 117
CAC1049 CAC1049 Uncharacterized conserved protein,ortholog of YaaR B.subtilis (NCBI ptt file) 117, 158
CAC1272 CAC1272 Predicted membrane protein (NCBI ptt file) 106, 215
CAC1279 hemN Coproporphyrinogen III oxidase (NCBI ptt file) 3, 106
CAC1317 CAC1317 Potassium channel subunit (NCBI ptt file) 117, 344
CAC1528 CAC1528 Predicted membrane protein (NCBI ptt file) 117, 336
CAC1543 CAC1543 Lactate dehydrogenase (NCBI ptt file) 117, 265
CAC1614 CAC1614 Predicted glycosyltransferase (NCBI ptt file) 69, 117
CAC1760 CAC1760 Signal peptidase I (NCBI ptt file) 106, 194
CAC1821 purB Adenylosuccinate lyase (NCBI ptt file) 106, 297
CAC1852 CAC1852 Magnesium and cobalt transport protein (NCBI ptt file) 106, 346
CAC1858 CAC1858 MoxR-like ATPase (NCBI ptt file) 64, 106
CAC1911 CAC1911 Hypothetical protein (NCBI ptt file) 117, 345
CAC1921 CAC1921 Hypothetical protein (NCBI ptt file) 54, 117
CAC1922 CAC1922 Hypothetical protein (NCBI ptt file) 117, 246
CAC1948 CAC1948 Hypothetical protein (NCBI ptt file) 117, 261
CAC1949 CAC1949 Possible TPR-repeat contaning protein (NCBI ptt file) 117, 261
CAC1950 CAC1950 Hypothetical protein (NCBI ptt file) 117, 345
CAC2253 CAC2253 Membrane-associated sensory histidine kinase-like ATPase (NCBI ptt file) 82, 106
CAC2265 CAC2265 Uncharacterized conserved membrane protein (NCBI ptt file) 106, 297
CAC2266 CAC2266 Uncharacterized conserved membrane protein (fragment) (NCBI ptt file) 106, 297
CAC2370 CAC2370 Uncharacterized protein, YrfI family (NCBI ptt file) 106, 194
CAC2371 CAC2371 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 106, 194
CAC2397 CAC2397 Hypothetical protein (NCBI ptt file) 106, 296
CAC2418 CAC2418 Uncharacterized conserved membrane protein (NCBI ptt file) 117, 158
CAC2432 CAC2432 Predicted permease (NCBI ptt file) 82, 106
CAC2608 CAC2608 Trancriptional regulator of AraC family (NCBI ptt file) 117, 158
CAC2658 glnA Glutamine synthetase type III (NCBI ptt file) 99, 106
CAC2696 CAC2696 Predicted membrane protein (NCBI ptt file) 117, 346
CAC2907 CAC2907 Glycosyltransferase (NCBI ptt file) 13, 117
CAC3010 CAC3010 ATP-dependent RNA helicase (superfamily II), YDBR B.subtilis ortholog (NCBI ptt file) 84, 106
CAC3099 truA Pseudouridylate synthase, TRUA (NCBI ptt file) 106, 255
CAC3100 CAC3100 Predicted permease (Cobalt permease subfamily) (NCBI ptt file) 84, 106
CAC3228 CAC3228 Predicted membrane protein (NCBI ptt file) 5, 117
CAC3611 CAC3611 Regulatory protein related to malT, positive regulator of mal regulon (ATPase and HTH-type DNA-binding domain) (NCBI ptt file) 117, 158
CAC3675 CAC3675 Hypothetical secreted protein (NCBI ptt file) 106, 151
CAC3683 CAC3683 Penicillin-binding protein 2 (serine-type D-Ala-D-Ala carboxypeptidase) (NCBI ptt file) 117, 286
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 CAC0584
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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