Organism : Clostridium acetobutylicum | Module List :
CAC3236

Possible transcriptional regulator from YAEG/LRPR family (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Regulator of polyketide synthase expression cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3236
(Mouseover regulator name to see its description)

CAC3236 is regulated by 21 influences and regulates 9 modules.
Regulators for CAC3236 (21)
Regulator Module Operator
CAC0360 247 tf
CAC0459 247 tf
CAC2242 247 tf
CAC2254 247 tf
CAC3236 247 tf
CAC3349 247 tf
CAC3481 247 tf
CAC3509 247 tf
CAC3525 247 tf
CAC3649 247 tf
CAC0201 312 tf
CAC0859 312 tf
CAC0933 312 tf
CAC1032 312 tf
CAC1578 312 tf
CAC2254 312 tf
CAC2939 312 tf
CAC3166 312 tf
CAC3345 312 tf
CAC3466 312 tf
CAC3488 312 tf

Warning: CAC3236 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
7146 2.30e-04 ttaGGAGg
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7147 4.00e-02 c.G.GgTaCcGcg
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7276 1.40e-02 aaGGaGG
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7277 2.50e+03 tAaaag.g.GagaAA
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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 CAC3236

CAC3236 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Regulator of polyketide synthase expression cog/ cog
Module neighborhood information for CAC3236

CAC3236 has total of 57 gene neighbors in modules 247, 312
Gene neighbors (57)
Gene Common Name Description Module membership
CAC0009 CAC0009 Uncharacterized conserved protein, ortholog of YRXA B.subtilis (NCBI ptt file) 62, 312
CAC0010 CAC0010 Uncharacterized conserved protein, possible metal-binding (NCBI ptt file) 283, 312
CAC0043 CAC0043 Hypothetical protein, CF-3 family (NCBI ptt file) 99, 312
CAC0044 CAC0044 Predicted membrane protein (NCBI ptt file) 264, 312
CAC0090 CAC0090 Xylanase/chitin deacetylase, NodB family (NCBI ptt file) 109, 312
CAC0122 cheY Chemotaxis respons regulator (cheY) (NCBI ptt file) 167, 247
CAC0132 CAC0132 Hypothetical protein (NCBI ptt file) 247, 270
CAC0134 CAC0134 Hypothetical protein, CF-19 family (NCBI ptt file) 62, 247
CAC0135 CAC0135 Hypothetical protein, CF-23 family (NCBI ptt file) 13, 247
CAC0354 CAC0354 Uncharacterized membrane protein (NCBI ptt file) 279, 312
CAC0419 CAC0419 Predicted membrane protein (NCBI ptt file) 247, 351
CAC0420 CAC0420 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 185, 247
CAC0477 CAC0477 AP superfamily (NCBI ptt file) 247, 258
CAC0487 CAC0487 Uncharacterized protein, ortholog of Thermotoga maritima (4981823) (NCBI ptt file) 247, 259
CAC0618 CAC0618 Uncharacterised permease, similar to ABC transporter (permease) (NCBI ptt file) 40, 312
CAC0626 trpS Tryptophan-tRNA synthetase, trpS (NCBI ptt file) 247, 296
CAC0726 CAC0726 Ribose 5-phosphate isomerase RpiB (NCBI ptt file) 288, 312
CAC0915 CAC0915 Endoglucanase A precursor (endo-1,4-beta-glucanase) (cellulase A), secreted; dockerin domain (NCBI ptt file) 26, 312
CAC1271 CAC1271 ComC competence related protein (NCBI ptt file) 190, 312
CAC1277 CAC1277 Predicted membrane protein (NCBI ptt file) 312, 328
CAC1495 CAC1495 Enzyme of dihydrofolate reductase family, ortholog YWFD B.subtilis (NCBI ptt file) 5, 247
CAC1635 CAC1635 Predicted nucleic acid binding protein, containing 2 S1 domains, YITL B.subtilis ortholog (NCBI ptt file) 109, 312
CAC1829 CAC1829 Predicted inactivated Zn-dependent peptidase, PMBA ortholog (NCBI ptt file) 312, 315
CAC1860 CAC1860 Predicted flavodoxin oxidoreductase (NCBI ptt file) 62, 312
CAC1956 CAC1956 Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file) 102, 312
CAC2033 CAC2033 Hypothetical protein (NCBI ptt file) 99, 312
CAC2037 CAC2037 Hypothetical protein, CF-39 family (NCBI ptt file) 109, 312
CAC2038 CAC2038 Hypothetical protein, CF-23 family (NCBI ptt file) 273, 312
CAC2096 CAC2096 Hypothetical protein (NCBI ptt file) 69, 312
CAC2098 CAC2098 Hypothetical protein (NCBI ptt file) 267, 312
CAC2102 CAC2102 Prepilin peptidase (NCBI ptt file) 54, 312
CAC2242 CAC2242 Predicted transcriptional regulator, arsE family (NCBI ptt file) 214, 247
CAC2251 CAC2251 Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file) 123, 312
CAC2348 CAC2348 Glycosyltransferase (NCBI ptt file) 13, 312
CAC2431 CAC2431 Alkaline phosphatase superfamily enzyme (NCBI ptt file) 62, 312
CAC2434 CAC2434 Membrane associatehistidine kinase with HAMP domain (NCBI ptt file) 44, 312
CAC2491 CAC2491 Predicted acetyltransferase (NCBI ptt file) 179, 312
CAC2719 CAC2719 Ethanolamin permease (NCBI ptt file) 111, 312
CAC2824 CAC2824 N-terminal HKD family nuclease fused to DNA/RNA helicases of superfamily II,conserved in Streptomyces (NCBI ptt file) 154, 247
CAC2831 CAC2831 Conserved membrane protein, YccA family (NCBI ptt file) 312, 366
CAC2902 CAC2902 Isopentenyl monophosphate kinase, IPK (NCBI ptt file) 66, 247
CAC2908 CAC2908 Spore coat protein cotS related (NCBI ptt file) 190, 312
CAC2910 CAC2910 Spore coat protein cotS related (NCBI ptt file) 190, 312
CAC2973 kdgA 2-keto-3-deoxy-6-phosphogluconate aldolase, eda/kdgA (NCBI ptt file) 108, 247
CAC3222 gcaD UDP-N-acetylglucosamine pyrophosphorylase (NCBI ptt file) 255, 312
CAC3232 CAC3232 Hypothetical protein (NCBI ptt file) 62, 247
CAC3236 CAC3236 Possible transcriptional regulator from YAEG/LRPR family (NCBI ptt file) 247, 312
CAC3237 msmX Multiple sugar-binding ABC-transporter, MSMX ATP-binding protein (NCBI ptt file) 301, 312
CAC3380 CAC3380 Metallo-beta-lactamase superfamily hydrolase (NCBI ptt file) 108, 247
CAC3481 CAC3481 Transcriptional regulator, AcrR family (NCBI ptt file) 167, 247
CAC3491 CAC3491 Protein, related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) (NCBI ptt file) 312, 341
CAC3524 CAC3524 Hypothetical protein, CF-7 family (NCBI ptt file) 226, 247
CAC3531 CAC3531 IS605/IS200-like transposase (NCBI ptt file) 190, 247
CAC3562 CAC3562 HD superfamily hydrolase (NCBI ptt file) 127, 247
CAC3563 CAC3563 Mismatch repair protein MutS-like ATPase (NCBI ptt file) 247, 335
CAC3649 spoVT Possible stage V sporulation protein T, transcriptional regulator AbrB homolog (NCBI ptt file) 108, 247
CAC3677 kdpE KDP operon transcriptional regulatory protein KdpE (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 108, 247
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 CAC3236
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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