Organism : Clostridium acetobutylicum | Module List :
CAC3403

Predicted membrane protein (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
ABC-type multidrug transport system, permease component cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3403
(Mouseover regulator name to see its description)

CAC3403 is regulated by 28 influences and regulates 0 modules.
Regulators for CAC3403 (28)
Regulator Module Operator
CAC0019 317 tf
CAC0393 317 tf
CAC0766 317 tf
CAC1483 317 tf
CAC1689 317 tf
CAC1698 317 tf
CAC2306 317 tf
CAC2307 317 tf
CAC3345 317 tf
CAC3424 317 tf
CAC3646 317 tf
CAC3649 317 tf
CAC0081 118 tf
CAC0299 118 tf
CAC0310 118 tf
CAC0531 118 tf
CAC1430 118 tf
CAC1509 118 tf
CAC1689 118 tf
CAC1786 118 tf
CAC1946 118 tf
CAC2236 118 tf
CAC2259 118 tf
CAC2552 118 tf
CAC3063 118 tf
CAC3214 118 tf
CAC3361 118 tf
CAC3669 118 tf

Warning: CAC3403 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
6888 2.70e-03 gGaGGaAt
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6889 1.60e+04 tAtag.Tt.gaAAgtagcTtc
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7286 2.00e+01 AGg.Gg
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7287 1.60e+04 GCGGaTG
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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 CAC3403

CAC3403 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
ABC-type multidrug transport system, permease component cog/ cog
Module neighborhood information for CAC3403

CAC3403 has total of 40 gene neighbors in modules 118, 317
Gene neighbors (40)
Gene Common Name Description Module membership
CAC0077 CAC0077 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 297, 317
CAC0196 CAC0196 NADH-dependent flavine oxidoreductase (NCBI ptt file) 142, 317
CAC0280 CAC0280 Molybdate transport system, permease component (NCBI ptt file) 317, 363
CAC0609 CAC0609 Cyclic beta 1-2 glucan synthetase (NCBI ptt file) 118, 188
CAC0653 CAC0653 Response regulator (CheY-like receiver domain and HTH DNA binding domain) (NCBI ptt file) 294, 317
CAC0654 CAC0654 Sensory transduction histidine kinase (NCBI ptt file) 294, 317
CAC0686 CAC0686 Spore cortex-lytic enzyme prepeptide; peptodoglycan-binding domain (NCBI ptt file) 118, 341
CAC0765 CAC0765 Fe-S oxidoreductase (NCBI ptt file) 116, 317
CAC0769 CAC0769 Uncharacterized conserved protein (NCBI ptt file) 118, 314
CAC0852 CAC0852 Amino acid permease (NCBI ptt file) 115, 317
CAC0868 CAC0868 Predicted membrane protein (NCBI ptt file) 118, 304
CAC1003 CAC1003 Superfamily I DNA helicase (rep-like helicase) (NCBI ptt file) 267, 317
CAC1053 CAC1053 LPS glycosyltransferase (NCBI ptt file) 29, 317
CAC1097 CAC1097 Hypothetical protein (NCBI ptt file) 297, 317
CAC1308 CAC1308 Uncharacterized low-complexity protein, related to YISX/YYBG B.subtilis (NCBI ptt file) 51, 317
CAC1355 CAC1355 Transcriptional antiterminator (BglG family) (NCBI ptt file) 153, 317
CAC1423 CAC1423 Predicted dehydrogenase of short-chain alcohol dehydrogenase family, ortholog of YHDF B.subtilis (NCBI ptt file) 118, 300
CAC1442 CAC1442 Hypothetical protein (NCBI ptt file) 270, 317
CAC1483 CAC1483 Predicted transcriptional regulator (NCBI ptt file) 100, 317
CAC1486 CAC1486 Uncharacterized protein, ortholog of YKUS B.subtilis (NCBI ptt file) 118, 367
CAC1520 CAC1520 Hypothetical protein (NCBI ptt file) 118, 279
CAC1653 CAC1653 Predicted glycosyltransferases involved in cell wall biogenesis (NCBI ptt file) 73, 118
CAC1706 CAC1706 Phosphate permease (NCBI ptt file) 118, 245
CAC1707 CAC1707 Permease component of ATP-dependent phosphate uptake system (NCBI ptt file) 118, 245
CAC1982 CAC1982 Predicted membrane protein (NCBI ptt file) 51, 317
CAC2097 CAC2097 Hypothetical protein (NCBI ptt file) 270, 317
CAC2303 CAC2303 Stage V sporulation AE, SpoVAE (fragment) (NCBI ptt file) 22, 118
CAC2305 SpoVAC Stage V sporulation AC, SpoVAC (NCBI ptt file) 110, 118
CAC2468 CAC2468 Predicted acetyltransferase (NCBI ptt file) 110, 317
CAC2668 CAC2668 Hypothetical protein (NCBI ptt file) 270, 317
CAC2981 CAC2981 Mannose-1-phosphate guanyltransferase (pyrophosphorylase domain and phosphomannomutase domain) (NCBI ptt file) 118, 123
CAC3016 CAC3016 Uncharacterized conserved membrane protein (NCBI ptt file) 95, 118
CAC3077 CAC3077 Uncharacterized FAD-dependent dehydrogenase (NCBI ptt file) 118, 142
CAC3213 CAC3213 Possible stage V sporulation protein B, predicted transporter (NCBI ptt file) 86, 118
CAC3245 CAC3245 Subtilisin like protease (two fused domains) (NCBI ptt file) 118, 330
CAC3357 CAC3357 Hypothetical protein (NCBI ptt file) 118, 174
CAC3402 CAC3402 Dipeptidyl aminopeptidase/acylaminoacyl-peptidase related protein (NCBI ptt file) 118, 317
CAC3403 CAC3403 Predicted membrane protein (NCBI ptt file) 118, 317
CAC3660 CAC3660 Uncharacterized protein, homolog of Desulfovibrio gigas (gi:6978031) (NCBI ptt file) 100, 317
CAC3684 CAC3684 Polygalacturonase (NCBI ptt file) 22, 118
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 CAC3403
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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