Organism : Clostridium acetobutylicum | Module List :
CAC1071

Transcriptional regulator, AcrR family (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1071
(Mouseover regulator name to see its description)

CAC1071 is regulated by 19 influences and regulates 3 modules.
Regulators for CAC1071 (19)
Regulator Module Operator
CAC0144 65 tf
CAC0189 65 tf
CAC0255 65 tf
CAC0426 65 tf
CAC2768 65 tf
CAC3037 65 tf
CAC3433 65 tf
CAC3472 65 tf
CAC3475 65 tf
CAC0189 357 tf
CAC0254 357 tf
CAC0255 357 tf
CAC0445 357 tf
CAC0977 357 tf
CAC1675 357 tf
CAC2236 357 tf
CAC2471 357 tf
CAC3429 357 tf
CAC3472 357 tf

Warning: CAC1071 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
6784 4.20e-02 GGaGGatT
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6785 2.10e+03 gttTtaGctaTatga
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7366 2.40e-04 tGgAGGgt
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7367 2.10e+04 aGAGCG
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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 CAC1071

Warning: No Functional annotations were found!

Module neighborhood information for CAC1071

CAC1071 has total of 34 gene neighbors in modules 65, 357
Gene neighbors (34)
Gene Common Name Description Module membership
CAC0223 CAC0223 Predicted N6-adenine-specific DNA methylase (NCBI ptt file) 65, 258
CAC0335 CAC0335 Hypothetical protein, CF-7 family (NCBI ptt file) 65, 230
CAC0361 kduD 2 deoxy-D-gluconate 3-dehydrogenase (NCBI ptt file) 65, 240
CAC0395 kdgK 2-keto-3-deoxygluconate kinase (gene kdgK) (NCBI ptt file) 43, 65
CAC0396 CAC0396 3-hexulose-6-phosphate synthase (D-arabino-3-hexulose-6-phosphate formaldehyde lyase) (NCBI ptt file) 343, 357
CAC0534 pps Phosphoenolpyruvate synthase (gene pps) (NCBI ptt file) 65, 301
CAC0674 CAC0674 L-serine dehydratase, alpha chain (NCBI ptt file) 19, 357
CAC0705 CAC0705 Sugar ABC transporter, permease protein (NCBI ptt file) 65, 123
CAC0843 CAC0843 Ribonuclease precursor (barnase), secreted. (NCBI ptt file) 65, 67
CAC0845 CAC0845 Ferritin-like protein Rsg (NCBI ptt file) 65, 363
CAC0864 CAC0864 Histidine kinase-like ATPase (NCBI ptt file) 65, 258
CAC0887 adeC Adenine deaminase (NCBI ptt file) 65, 241
CAC0905 CAC0905 Uncharacterized NAD(FAD)-dependent dehydrogenase (NCBI ptt file) 65, 154
CAC1071 CAC1071 Transcriptional regulator, AcrR family (NCBI ptt file) 65, 357
CAC1366 CAC1366 Predicted membrane protein (NCBI ptt file) 234, 357
CAC1372 cobT Cobalamin biosynthesis enzyme CobT (NCBI ptt file) 55, 65
CAC1519 CAC1519 Predicted permease (NCBI ptt file) 253, 357
CAC1773 sacC Levanase (NCBI ptt file) 98, 357
CAC1863 CAC1863 Hypothetical protein (NCBI ptt file) 336, 357
CAC2420 CAC2420 Methyl-accepting chemotaxis protein (NCBI ptt file) 65, 357
CAC2503 CAC2503 Hypothetical protein (NCBI ptt file) 65, 208
CAC2596 CAC2596 Rieske FeS-domain containing oxidoreductase (NCBI ptt file) 65, 150
CAC2947 topB Topoisomerase B (NCBI ptt file) 65, 154
CAC2970 PatB PLP-dependent aminotransferase, (NCBI ptt file) 337, 357
CAC3011 CAC3011 Predicted membrane protein (NCBI ptt file) 65, 115
CAC3035 CAC3035 HAD superfamily hydrolase (NCBI ptt file) 65, 338
CAC3407 CAC3407 Acyl-CoA thioesterase 1 (NCBI ptt file) 46, 357
CAC3419 CAC3419 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 220, 357
CAC3472 CAC3472 Protein containing transcriptional regulator domain (NCBI ptt file) 349, 357
CAC3511 CAC3511 Membrane associated methyl-accepting chemotaxis protein with HAMP domain (NCBI ptt file) 210, 357
CAC3571 fabZ Hydroxymyristoyl-(acyl carrier protein) dehydratase (NCBI ptt file) 65, 91
CAC3642 CAC3642 Oligopeptide ABC transporter, ATPase component (NCBI ptt file) 65, 217
CAC3655 CAC3655 Heavy-metal transporting P-type ATPase (NCBI ptt file) 108, 357
CAC3669 CAC3669 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 65, 137
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 CAC1071
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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