Organism : Clostridium acetobutylicum | Module List :
CAC3638

Oligopeptide ABC transporter, permease component (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
alkaline phosphatase activity go/ molecular_function
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3638
(Mouseover regulator name to see its description)

CAC3638 is regulated by 19 influences and regulates 0 modules.
Regulators for CAC3638 (19)
Regulator Module Operator
CAC1695 42 tf
CAC2242 42 tf
CAC2307 42 tf
CAC3088 42 tf
CAC3646 42 tf
CAC3649 42 tf
CAC3729 42 tf
CAC0189 269 tf
CAC0289 269 tf
CAC0681 269 tf
CAC1689 269 tf
CAC1696 269 tf
CAC2242 269 tf
CAC2306 269 tf
CAC2307 269 tf
CAC3142 269 tf
CAC3646 269 tf
CAC3649 269 tf
CAC3729 269 tf

Warning: CAC3638 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
6738 3.60e-01 GGGGAtg
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6739 4.40e+03 AGGAGG
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7190 4.80e-06 GGggGat
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7191 6.80e+03 AccTTTttTGg
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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 CAC3638

CAC3638 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
alkaline phosphatase activity go/ molecular_function
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
Module neighborhood information for CAC3638

CAC3638 has total of 27 gene neighbors in modules 42, 269
Gene neighbors (27)
Gene Common Name Description Module membership
CAC0353 CAC0353 2,3-cyclic-nucleotide 2'phosphodiesterase (duplication) (NCBI ptt file) 42, 269
CAC0489 CAC0489 Holo-acyl-carrier protein synthase (NCBI ptt file) 29, 42
CAC0746 CAC0746 Secreted protease metal-dependent protease (NCBI ptt file) 269, 345
CAC1044 CAC1044 NADH:flavin oxidoreductase, possible NADH oxidase (NCBI ptt file) 42, 164
CAC1674 gltB Small subunit of NADPH-dependent glutamate synthase (NCBI ptt file) 29, 269
CAC1694 CAC1694 Sigma factor E processing enzyme, SpoIIGA (NCBI ptt file) 42, 199
CAC1751 smc Chromosome segregation SMC protein, ATPase (NCBI ptt file) 213, 269
CAC1752 ftsY Signal recognition particle GTPase, FtsY (NCBI ptt file) 29, 269
CAC1811 CAC1811 Periplasmic serine protease, YMFB B.subtilis ortholog (NCBI ptt file) 142, 269
CAC1812 CAC1812 Sporulation protein SpoIIIE, DNA segregation ATPase (NCBI ptt file) 29, 269
CAC1841 CAC1841 Uncharacterized protein, related to Spore coat protein CotS (NCBI ptt file) 73, 269
CAC2237 glgC ADP-glucose pyrophosphorylase (NCBI ptt file) 42, 184
CAC2238 glgC ADP-glucose pyrophosphorylase (NCBI ptt file) 42, 269
CAC2239 glgA Glycogen synthase, glgA (NCBI ptt file) 42, 269
CAC2507 CAC2507 Predicted membrane protein (NCBI ptt file) 29, 269
CAC2517 nrpE Extracellular neutral metalloprotease, NPRE (NCBI ptt file) 269, 305
CAC2623 CAC2623 Possible sensorory transduction protein, containing AAA ATPase domain, TPR repeats domain, GGDEF domain and GAF domain (NCBI ptt file) 134, 269
CAC3205 spoIIE Stage II sporulation protein E, serine phosphatase family (NCBI ptt file) 42, 367
CAC3229 CAC3229 NADH:flavin oxidoreductases, Old Yellow Enzyme family (NCBI ptt file) 42, 293
CAC3633 CAC3633 Hypothetical protein (NCBI ptt file) 42, 269
CAC3634 CAC3634 Oligopeptide ABC transporter, periplasmic substrate-binding component (NCBI ptt file) 42, 269
CAC3635 CAC3635 Oligopeptide ABC transporter, ATPase component (NCBI ptt file) 42, 269
CAC3636 CAC3636 Oligopeptide ABC transporter, ATPase component (NCBI ptt file) 42, 269
CAC3637 CAC3637 Oligopeptide ABC transporter, permease component (NCBI ptt file) 42, 269
CAC3638 CAC3638 Oligopeptide ABC transporter, permease component (NCBI ptt file) 42, 269
CAC3639 CAC3639 CRO repressor-like DNA-binding protein (NCBI ptt file) 42, 269
CAC3646 CAC3646 Predicted transcriptional regulator, containing DNA-binding domain of xre family (NCBI ptt file) 60, 269
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 CAC3638
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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