Organism : Clostridium acetobutylicum | Module List :
CAC3494

Transcription regulator, YOBV B.subtilis homolog (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3494
(Mouseover regulator name to see its description)

CAC3494 is regulated by 17 influences and regulates 11 modules.
Regulators for CAC3494 (17)
Regulator Module Operator
CAC0113 344 tf
CAC0457 344 tf
CAC0859 344 tf
CAC1578 344 tf
CAC3406 344 tf
CAC3413 344 tf
CAC3494 344 tf
CAC3512 344 tf
CAC0382 102 tf
CAC1465 102 tf
CAC1536 102 tf
CAC1689 102 tf
CAC1965 102 tf
CAC3192 102 tf
CAC3488 102 tf
CAC3494 102 tf
CAC3651 102 tf
Regulated by CAC3494 (11)
Module Residual Genes
17 0.21 12
69 0.46 29
102 0.55 24
115 0.43 26
158 0.39 23
190 0.46 30
199 0.26 13
308 0.21 12
344 0.40 20
361 0.31 20
364 0.19 12
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
6856 2.10e-05 aaAGGaGg
Loader icon
6857 1.00e+04 cCAaGGGC
Loader icon
7340 2.50e+03 CcTGgC
Loader icon
7341 2.60e+01 AGGaGtga
Loader icon
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 CAC3494

CAC3494 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC3494

CAC3494 has total of 43 gene neighbors in modules 102, 344
Gene neighbors (43)
Gene Common Name Description Module membership
CAC0036 CAC0036 Predicted membrane protein, containing FHA domain (NCBI ptt file) 102, 183
CAC0045 CAC0045 TPR-repeat-containing protein (NCBI ptt file) 102, 264
CAC0249 CAC0249 Glyoxalase I (glyoxalase family) (NCBI ptt file) 102, 332
CAC0347 CAC0347 Hypothetical protein (NCBI ptt file) 309, 344
CAC0381 CAC0381 Methyl-accepting chemotaxis protein (NCBI ptt file) 74, 344
CAC0457 CAC0457 Transcriptional regulator, AcrR family (NCBI ptt file) 74, 344
CAC0511 CAC0511 Predicted P-loop containing kinase, similar to B.subtilis yvcJ (NCBI ptt file) 102, 291
CAC0530 CAC0530 Hypothetical protein (NCBI ptt file) 102, 353
CAC0573 CAC0573 Uncharacterized protein, homolog YvqG B.subtilis (NCBI ptt file) 102, 251
CAC0578 metH Cobalamine-dependent methionine synthase I (methyltransferase and cobalamine-binding domain) (NCBI ptt file) 102, 146
CAC0583 CAC0583 CBIK protein (chain A, anaerobic cobalt chelatase) (NCBI ptt file) 117, 344
CAC0647 CAC0647 Predicted membrane protein (NCBI ptt file) 149, 344
CAC0814 CAC0814 3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI ptt file) 244, 344
CAC0859 CAC0859 Ortholog putative anti-SigV factor [Bacillus subtilis] (NCBI ptt file) 69, 344
CAC0881 CAC0881 Hypothetical protein (NCBI ptt file) 267, 344
CAC0984 CAC0984 ABC transporter, ATP-binding protein (NCBI ptt file) 102, 146
CAC1077 CAC1077 Putative translation initiation inhibitor (NCBI ptt file) 102, 179
CAC1145 CAC1145 Hypothetical protein (NCBI ptt file) 326, 344
CAC1317 CAC1317 Potassium channel subunit (NCBI ptt file) 117, 344
CAC1350 CAC1350 Hypothetical protein (NCBI ptt file) 102, 190
CAC1645 CAC1645 Ankyrin repeats containing protein (NCBI ptt file) 69, 102
CAC1784 smf DNA uptake protein (NCBI ptt file) 39, 102
CAC1846 motA Flagellar motor component MotA (NCBI ptt file) 102, 123
CAC1956 CAC1956 Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file) 102, 312
CAC2057 CAC2057 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 102, 207
CAC2291 CAC2291 Hypothetical protein (NCBI ptt file) 86, 102
CAC2402 CAC2402 TPR repeats containing protein (NCBI ptt file) 69, 102
CAC2506 CAC2506 SpoIID-like domain containing protein; peptidoglycan-binding domain (NCBI ptt file) 102, 190
CAC2636 CAC2636 Predicted GTPase, YSXC B.subtilis ortholog (NCBI ptt file) 102, 123
CAC2705 CAC2705 Uncharacterized membrane protein, homolog of Aquifex (GI:2984271) (NCBI ptt file) 74, 344
CAC2720 CAC2720 Sensory protein containing histidine kinase, PAS anf GAF domains (NCBI ptt file) 102, 123
CAC2756 CAC2756 MDR-type ABC transporter (membrane associated ATPase) (NCBI ptt file) 102, 176
CAC2776 CAC2776 Hypothetical protein (NCBI ptt file) 62, 102
CAC2863 CAC2863 Predicted membrane protein (NCBI ptt file) 102, 279
CAC2877 CAC2877 ABC-type iron (III) transport system, ATPase component (NCBI ptt file) 69, 344
CAC3085 CAC3085 TPR-repeat-containing protein; Cell-adhesion domain (NCBI ptt file) 225, 344
CAC3086 CAC3086 Protein containing cell adhesion domain (NCBI ptt file) 225, 344
CAC3168 CAC3168 Predicted membrane protein (NCBI ptt file) 62, 344
CAC3406 CAC3406 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 140, 344
CAC3413 CAC3413 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 89, 344
CAC3433 CAC3433 Transcriptional regulators, AcrR family (NCBI ptt file) 150, 344
CAC3434 CAC3434 Hypothetical protein (NCBI ptt file) 205, 344
CAC3494 CAC3494 Transcription regulator, YOBV B.subtilis homolog (NCBI ptt file) 102, 344
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 CAC3494
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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