Organism : Clostridium acetobutylicum | Module List :
CAC2636

Predicted GTPase, YSXC B.subtilis ortholog (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Predicted GTPase cog/ cog
GTP binding go/ molecular_function
intracellular go/ cellular_component
Gram-negative-bacterium-type cell wall go/ cellular_component
ferrous iron transmembrane transporter activity go/ molecular_function
ferrous iron transport go/ biological_process
integral to membrane go/ cellular_component
GTPase_YsxC tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2636
(Mouseover regulator name to see its description)

CAC2636 is regulated by 18 influences and regulates 0 modules.
Regulators for CAC2636 (18)
Regulator Module Operator
CAC0807 123 tf
CAC1032 123 tf
CAC1843 123 tf
CAC1869 123 tf
CAC2768 123 tf
CAC3406 123 tf
CAC3418 123 tf
CAC3488 123 tf
CAC3502 123 tf
CAC0382 102 tf
CAC1465 102 tf
CAC1536 102 tf
CAC1689 102 tf
CAC1965 102 tf
CAC3192 102 tf
CAC3488 102 tf
CAC3494 102 tf
CAC3651 102 tf

Warning: CAC2636 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
6856 2.10e-05 aaAGGaGg
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6857 1.00e+04 cCAaGGGC
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6898 8.40e-04 aGGagg
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6899 6.20e+02 cctCttcATACTcCattgg
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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 CAC2636

CAC2636 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Predicted GTPase cog/ cog
GTP binding go/ molecular_function
intracellular go/ cellular_component
Gram-negative-bacterium-type cell wall go/ cellular_component
ferrous iron transmembrane transporter activity go/ molecular_function
ferrous iron transport go/ biological_process
integral to membrane go/ cellular_component
GTPase_YsxC tigr/ tigrfam
Module neighborhood information for CAC2636

CAC2636 has total of 45 gene neighbors in modules 102, 123
Gene neighbors (45)
Gene Common Name Description Module membership
CAC0036 CAC0036 Predicted membrane protein, containing FHA domain (NCBI ptt file) 102, 183
CAC0045 CAC0045 TPR-repeat-containing protein (NCBI ptt file) 102, 264
CAC0172 CAC0172 Predicted membrane protein (NCBI ptt file) 123, 328
CAC0249 CAC0249 Glyoxalase I (glyoxalase family) (NCBI ptt file) 102, 332
CAC0511 CAC0511 Predicted P-loop containing kinase, similar to B.subtilis yvcJ (NCBI ptt file) 102, 291
CAC0530 CAC0530 Hypothetical protein (NCBI ptt file) 102, 353
CAC0573 CAC0573 Uncharacterized protein, homolog YvqG B.subtilis (NCBI ptt file) 102, 251
CAC0574 CAC0574 Pectate lyase H (FS) (NCBI ptt file) 123, 256
CAC0578 metH Cobalamine-dependent methionine synthase I (methyltransferase and cobalamine-binding domain) (NCBI ptt file) 102, 146
CAC0705 CAC0705 Sugar ABC transporter, permease protein (NCBI ptt file) 65, 123
CAC0813 CAC0813 Hypothetical protein (NCBI ptt file) 123, 150
CAC0926 CAC0926 TPR-repeat-containing protein (NCBI ptt file) 123, 270
CAC0984 CAC0984 ABC transporter, ATP-binding protein (NCBI ptt file) 102, 146
CAC1077 CAC1077 Putative translation initiation inhibitor (NCBI ptt file) 102, 179
CAC1199 CAC1199 Hypothetical protein (NCBI ptt file) 86, 123
CAC1350 CAC1350 Hypothetical protein (NCBI ptt file) 102, 190
CAC1446 CAC1446 Hypothetical protein (NCBI ptt file) 123, 270
CAC1580 CAC1580 Hypothetical protein (NCBI ptt file) 90, 123
CAC1645 CAC1645 Ankyrin repeats containing protein (NCBI ptt file) 69, 102
CAC1650 CAC1650 Hypothetical protein, CF-38 family (NCBI ptt file) 123, 270
CAC1784 smf DNA uptake protein (NCBI ptt file) 39, 102
CAC1844 CAC1844 Hypothetical protein (NCBI ptt file) 26, 123
CAC1845 motB Flagellar motor protein MotB (NCBI ptt file) 123, 137
CAC1846 motA Flagellar motor component MotA (NCBI ptt file) 102, 123
CAC1956 CAC1956 Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file) 102, 312
CAC2057 CAC2057 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 102, 207
CAC2251 CAC2251 Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file) 123, 312
CAC2267 CAC2267 Hypothetical protein (NCBI ptt file) 111, 123
CAC2291 CAC2291 Hypothetical protein (NCBI ptt file) 86, 102
CAC2339 CAC2339 Uncharacterized protein, YBBK B.subtilis ortholog (NCBI ptt file) 76, 123
CAC2402 CAC2402 TPR repeats containing protein (NCBI ptt file) 69, 102
CAC2506 CAC2506 SpoIID-like domain containing protein; peptidoglycan-binding domain (NCBI ptt file) 102, 190
CAC2586 CAC2586 Predicted membrane protein (NCBI ptt file) 123, 169
CAC2636 CAC2636 Predicted GTPase, YSXC B.subtilis ortholog (NCBI ptt file) 102, 123
CAC2702 CAC2702 Possible signal transduction protein (containing EAL, CBS and GGDEF domains) (NCBI ptt file) 123, 333
CAC2720 CAC2720 Sensory protein containing histidine kinase, PAS anf GAF domains (NCBI ptt file) 102, 123
CAC2756 CAC2756 MDR-type ABC transporter (membrane associated ATPase) (NCBI ptt file) 102, 176
CAC2776 CAC2776 Hypothetical protein (NCBI ptt file) 62, 102
CAC2811 CAC2811 Hypothetical protein, CF-17 family (NCBI ptt file) 123, 258
CAC2863 CAC2863 Predicted membrane protein (NCBI ptt file) 102, 279
CAC2981 CAC2981 Mannose-1-phosphate guanyltransferase (pyrophosphorylase domain and phosphomannomutase domain) (NCBI ptt file) 118, 123
CAC3256 CAC3256 Predicted acetyltransferase (NCBI ptt file) 123, 341
CAC3415 CAC3415 ABC-type multidrug/protein/lipid transport system, ATPase component (NCBI ptt file) 123, 208
CAC3494 CAC3494 Transcription regulator, YOBV B.subtilis homolog (NCBI ptt file) 102, 344
CAC3697 CAC3697 Uncharacterized, Zn-finger domain containing protein, YXKC B.subtilis homolog (NCBI ptt file) 123, 150
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 CAC2636
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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