Organism : Clostridium acetobutylicum | Module List :
CAC0708

Putative transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator, contains sigma factor-related N-terminal domain cog/ cog
carbohydrate binding go/ molecular_function
transcription regulator activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0708
(Mouseover regulator name to see its description)

CAC0708 is regulated by 19 influences and regulates 5 modules.
Regulators for CAC0708 (19)
Regulator Module Operator
CAC0183 20 tf
CAC0708 20 tf
CAC0768 20 tf
CAC0977 20 tf
CAC1753 20 tf
CAC2889 20 tf
CAC3216 20 tf
CAC3475 20 tf
CAC3579 20 tf
CAC0708 359 tf
CAC0832 359 tf
CAC1578 359 tf
CAC1695 359 tf
CAC1869 359 tf
CAC2254 359 tf
CAC2306 359 tf
CAC3166 359 tf
CAC3247 359 tf
CAC3518 359 tf

Warning: CAC0708 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
6694 3.60e-03 t.gagagGtgA
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6695 7.60e+02 AAaTACCTccaTTaC
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7368 1.10e+03 CCCC.TA
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7369 5.40e+03 CAGGCG
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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 CAC0708

CAC0708 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator, contains sigma factor-related N-terminal domain cog/ cog
carbohydrate binding go/ molecular_function
transcription regulator activity go/ molecular_function
Module neighborhood information for CAC0708

CAC0708 has total of 46 gene neighbors in modules 20, 359
Gene neighbors (46)
Gene Common Name Description Module membership
CAC0113 CAC0113 Transcriptional regulator of sugar metabolism (NCBI ptt file) 20, 346
CAC0114 CAC0114 Predicted membrane protein (NCBI ptt file) 20, 286
CAC0116 CAC0116 Carbone-monoxide dehydrogenase, beta chain (NCBI ptt file) 20, 182
CAC0433 CAC0433 Methyl-accepting chemotaxis protein (NCBI ptt file) 20, 225
CAC0454 CAC0454 Predicted ATP transporter permease component (NCBI ptt file) 343, 359
CAC0650 CAC0650 Adenilate cyclase, class2 (thermophilic) (NCBI ptt file) 20, 348
CAC0700 cspR Predicted tRNA-methylase (SpoU class) (NCBI ptt file) 350, 359
CAC0701 CAC0701 Uncharacterised protein, DegV family (NCBI ptt file) 20, 58
CAC0708 CAC0708 Putative transcriptional regulator (NCBI ptt file) 20, 359
CAC0709 gapC Glyceraldehyde 3-phosphate dehydrogenase, gene gapC (NCBI ptt file) 10, 20
CAC0712 pgm 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gene (NCBI ptt file) 20, 292
CAC0826 CAC0826 Endoglucanase family 5 (NCBI ptt file) 151, 359
CAC0990 gltX Glutamyl-tRNA synthetase (NCBI ptt file) 20, 306
CAC1036 pykA Pyruvate kinase (NCBI ptt file) 348, 359
CAC1152 CAC1152 Hypothetical protein (NCBI ptt file) 16, 359
CAC1407 CAC1407 PTS system, beta-glucosides-specific IIABC component (NCBI ptt file) 282, 359
CAC1660 CAC1660 Butyrate kinase, buk (NCBI ptt file) 332, 359
CAC1677 CAC1677 Predicted permease (NCBI ptt file) 259, 359
CAC1693 ftsZ Cell division GTPase FtsZ (NCBI ptt file) 20, 233
CAC2056 CAC2056 Hypothetical protein (NCBI ptt file) 26, 359
CAC2095 CAC2095 Aminopeptidase P AMPP/PEPQ family enzyme, YQHT B.subtilis ortholog (NCBI ptt file) 20, 286
CAC2140 flgG Flagellar basal body rod protein (NCBI ptt file) 192, 359
CAC2215 fliY Flagellar switch protein FliY, contains CheC-like domain (NCBI ptt file) 122, 359
CAC2227 CAC2227 Phosphoserine phosphatase family enzyme (NCBI ptt file) 20, 286
CAC2255 CAC2255 Predicted permease (NCBI ptt file) 336, 359
CAC2264 glyA Glycine hydroxymethyltransferase (NCBI ptt file) 20, 286
CAC2292 CAC2292 Predicted membrane protein (NCBI ptt file) 282, 359
CAC2332 spsJ DTDP-D-glucose 4,6-dehydratase (NCBI ptt file) 20, 239
CAC2523 CAC2523 Glycosyltransferase (NCBI ptt file) 191, 359
CAC2633 CAC2633 Uncharaterized conserved protein, YOME B.subtilis ortholog (NCBI ptt file) 20, 58
CAC2655 CAC2655 Uncharacterized membrane-associated protein, DedA family (NCBI ptt file) 26, 359
CAC2732 CAC2732 ABC transporter, ATPase component (NCBI ptt file) 69, 359
CAC2771 CAC2771 Amino acid transporter (NCBI ptt file) 20, 286
CAC2779 CAC2779 Hypothetical protein (NCBI ptt file) 20, 259
CAC2780 CAC2780 Spore coat protein, cotF related (NCBI ptt file) 20, 259
CAC2889 rho Transcription termination factor rho (NCBI ptt file) 20, 239
CAC3097 rpsI Ribosomal protein S9 (NCBI ptt file) 20, 237
CAC3103 rplQ Ribosomal protein L17 (NCBI ptt file) 20, 59
CAC3225 murC UDP-N-acetylmuramate-alanine ligase (NCBI ptt file) 292, 359
CAC3247 CAC3247 Predicted transcriptional regulator, lacI/xre family (NCBI ptt file) 151, 359
CAC3272 CAC3272 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 285, 359
CAC3384 CAC3384 Protein chain release factor B (NCBI ptt file) 343, 359
CAC3435 CAC3435 Hypothetical protein (NCBI ptt file) 185, 359
CAC3518 CAC3518 Transcriptional regulators, AcrR family (NCBI ptt file) 225, 359
CAC3578 fabH 3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI ptt file) 20, 356
CAC3579 CAC3579 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 20, 356
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 CAC0708
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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