Organism : Clostridium acetobutylicum | Module List :
CAC0032

Transcriptional regulator TetR/AcrR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0032
(Mouseover regulator name to see its description)

CAC0032 is regulated by 16 influences and regulates 20 modules.
Regulators for CAC0032 (16)
Regulator Module Operator
CAC0032 1 tf
CAC0191 1 tf
CAC0197 1 tf
CAC1766 1 tf
CAC2242 1 tf
CAC2773 1 tf
CAC3413 1 tf
CAC3729 1 tf
CAC0023 179 tf
CAC0032 179 tf
CAC0465 179 tf
CAC0763 179 tf
CAC0863 179 tf
CAC1333 179 tf
CAC2476 179 tf
CAC2546 179 tf

Warning: CAC0032 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
6656 4.30e-01 ctTaTGtAccTttTTtATgTaAc
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6657 9.90e+01 gaAGGAGG
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7010 7.20e-04 tcCTCC
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7011 3.90e+03 cGACacCCC
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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 CAC0032

CAC0032 is enriched for 5 functions in 3 categories.
Module neighborhood information for CAC0032

CAC0032 has total of 40 gene neighbors in modules 1, 179
Gene neighbors (40)
Gene Common Name Description Module membership
CAC0023 CAC0023 Transcriptional regulator, LysR family (NCBI ptt file) 179, 266
CAC0032 CAC0032 Transcriptional regulator TetR/AcrR family (NCBI ptt file) 1, 179
CAC0153 CAC0153 Beta-phosphoglucomutase, putative (NCBI ptt file) 179, 302
CAC0180 appF Oligopeptide ABC transporter, ATP-binding protein (NCBI ptt file) 179, 278
CAC0334 CAC0334 Hypothetical protein, CF-21 family (NCBI ptt file) 1, 92
CAC0350 CAC0350 Hypothetical protein (NCBI ptt file) 11, 179
CAC0443 CAC0443 Methyl-accepting chemotaxis protein (NCBI ptt file) 1, 122
CAC0557 CAC0557 Predicted Zn-dependent protease with possible chaperone function (NCBI ptt file) 40, 179
CAC1038 CAC1038 Predicted metal-binding membrane protein (NCBI ptt file) 77, 179
CAC1077 CAC1077 Putative translation initiation inhibitor (NCBI ptt file) 102, 179
CAC1107 CAC1107 Hypothetical protein, CF-36 family (NCBI ptt file) 167, 179
CAC1142 uvrD ATP-dependent DNA helicase, uvrD-like (NCBI ptt file) 1, 173
CAC1196 CAC1196 Hypothetical protein (NCBI ptt file) 1, 173
CAC1197 CAC1197 Phage toprim domain containing protein, YorJ B.subtilis homolog (NCBI ptt file) 1, 173
CAC1202 CAC1202 Hypothetical protein (NCBI ptt file) 1, 173
CAC1203 CAC1203 Hypothetical protein (NCBI ptt file) 1, 173
CAC1204 CAC1204 Hypothetical protein (NCBI ptt file) 1, 173
CAC1205 CAC1205 Hypothetical protein (NCBI ptt file) 1, 173
CAC1221 CAC1221 Hypothetical protein (NCBI ptt file) 1, 89
CAC1248 minC Septum site-determining protein MinC (NCBI ptt file) 167, 179
CAC1428 CAC1428 Hypothetical protein (NCBI ptt file) 93, 179
CAC1432 CAC1432 Undecaprenyl pyrophosphate synthase related enzyme (NCBI ptt file) 95, 179
CAC1550 CAC1550 Methionine sulfoxide reductase C-terminal domain related protein, YPPQ ortholog (NCBI ptt file) 179, 320
CAC1556 CAC1556 Chitinase family protein (NCBI ptt file) 1, 165
CAC1557 CAC1557 Predicted acetyltransferase (NCBI ptt file) 1, 185
CAC1558 CAC1558 ABC-type transport system,membrane ATPase component (NCBI ptt file) 1, 346
CAC1853 CAC1853 Predicted membrane protein (NCBI ptt file) 179, 262
CAC2278 secD Preprotein translocase subunits SecD (NCBI ptt file) 8, 179
CAC2279 CAC2279 Heme biosynthesis (nirJ-2) family protein (NCBI ptt file) 8, 179
CAC2396 CAC2396 Predicted xylanase/chitin deacetylase (NCBI ptt file) 179, 253
CAC2491 CAC2491 Predicted acetyltransferase (NCBI ptt file) 179, 312
CAC2676 CAC2676 Predicted pseudouridylate synthase (NCBI ptt file) 72, 179
CAC2896 CAC2896 Uncharacterized protein, YPEB B.subtilis ortholog (NCBI ptt file) 59, 179
CAC2898 spoIIR Stage II sporulation protein R (NCBI ptt file) 24, 179
CAC2995 CAC2995 PTS system (Glucose-specific) component IIA (NCBI ptt file) 77, 179
CAC2998 CAC2998 TPR-repeat-containing protein (NCBI ptt file) 1, 122
CAC3001 CAC3001 Uncharacterized consrved protein, containing Zn finger (NCBI ptt file) 1, 276
CAC3351 CAC3351 Uncharacterized membrane protein, YCBP B.subtilis ortholog (NCBI ptt file) 1, 115
CAC3483 CAC3483 Nitroreductase family protein fused to ferredoxin domain (NCBI ptt file) 1, 169
CAC3496 CAC3496 Predicted transcriptional regulator (NCBI ptt file) 179, 341
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 CAC0032
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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