Organism : Clostridium acetobutylicum | Module List :
CAC3360

Transcriptional regulator, LysR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3360
(Mouseover regulator name to see its description)

CAC3360 is regulated by 20 influences and regulates 12 modules.
Regulators for CAC3360 (20)
Regulator Module Operator
CAC0032 277 tf
CAC0255 277 tf
CAC0422 277 tf
CAC0569 277 tf
CAC0863 277 tf
CAC1668 277 tf
CAC1698 277 tf
CAC1915 277 tf
CAC2071 277 tf
CAC2306 277 tf
CAC2768 277 tf
CAC3360 277 tf
CAC3443 277 tf
CAC3646 277 tf
CAC0465 176 tf
CAC0550 176 tf
CAC0876 176 tf
CAC1333 176 tf
CAC3360 176 tf
CAC3695 176 tf

Warning: CAC3360 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
7004 1.80e+00 gaggaGAG
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7005 1.40e+03 AAGCcC
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7206 1.50e+00 AaggGTGc
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7207 3.00e+03 AActgccgG.caCtcac.AgAaAC
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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 CAC3360

CAC3360 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC3360

CAC3360 has total of 44 gene neighbors in modules 176, 277
Gene neighbors (44)
Gene Common Name Description Module membership
CAC0022 asd Aspartate-semialdehyde dehydrogenase (NCBI ptt file) 176, 231
CAC0067 CAC0067 (FS) similar to ABC transporter (permease), YXDM B.subtilis ortholog (NCBI ptt file) 176, 246
CAC0130 CAC0130 Uncharacterized membrane protein, YTAF B.subtilis ortholog (NCBI ptt file) 176, 341
CAC0550 CAC0550 Possible sigma factor (NCBI ptt file) 176, 253
CAC0569 sacT SACPA operon antiterminator (sacT) (NCBI ptt file) 149, 277
CAC0606 CAC0606 C-terminal region cation efflux system protein CZCD (NCBI ptt file) 52, 277
CAC0632 CAC0632 Predicted phosphatase (NCBI ptt file) 52, 277
CAC0687 cysE Serine acetyltransferase (NCBI ptt file) 196, 277
CAC0691 CAC0691 Uncharacterized conserved protein, VanW of Enterococcus faecalis related (NCBI ptt file) 176, 253
CAC0693 CAC0693 Transcriptional regulator of the LacI family (NCBI ptt file) 176, 238
CAC0777 CAC0777 Acetyltransferase (the isoleucine patch superfamily) (NCBI ptt file) 176, 306
CAC0816 CAC0816 Lipase-esterase related protein (NCBI ptt file) 176, 209
CAC0902 CAC0902 Predicted membrane protein (NCBI ptt file) 134, 277
CAC0903 CAC0903 Sensory transduction histidine kinase (NCBI ptt file) 134, 277
CAC0983 CAC0983 Hypothetical protein (NCBI ptt file) 52, 277
CAC1023 nadC Nicotinate-nucleotide pyrophosphorylase (NCBI ptt file) 277, 280
CAC1045 CAC1045 Predicted permease (NCBI ptt file) 80, 176
CAC1068 CAC1068 Hypothetical protein, CF-25 family (NCBI ptt file) 176, 267
CAC1096 CAC1096 Uncharacterized protein, YjiN homolog (NCBI ptt file) 277, 348
CAC1215 CAC1215 Hypothetical protein (NCBI ptt file) 4, 176
CAC1263 CAC1263 HD superfamily hydrolase, yqeK B.subtilis ortholog (NCBI ptt file) 248, 277
CAC1312 CAC1312 Hypothetical protein (NCBI ptt file) 109, 176
CAC1434 CAC1434 Alkaline phosphatase superfamily protein (NCBI ptt file) 176, 276
CAC1554 CAC1554 Heavy-metal-associated domain (N-terminus) and membrane-bounded cytochrome biogenesis cycZ-like domain, possible membrane copper tolerance protein (NCBI ptt file) 176, 206
CAC1833 CAC1833 Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog (NCBI ptt file) 58, 277
CAC1854 CAC1854 Nudix (MutT) family hydrolase (NCBI ptt file) 209, 277
CAC1909 rnd Ribonuclease D (NCBI ptt file) 225, 277
CAC1910 CAC1910 Predicted membrane protein (NCBI ptt file) 225, 277
CAC1984 CAC1984 Predicted permease (NCBI ptt file) 176, 183
CAC2069 CAC2069 Hypothetical protein (NCBI ptt file) 152, 176
CAC2127 mraY Phospho-N-acetylmuramoyl-pentapeptide transferase, MraY (NCBI ptt file) 2, 277
CAC2505 CAC2505 Uncharacterized membrane protein, YXJN B.subtilis homolog (NCBI ptt file) 134, 176
CAC2751 CAC2751 Predicted acetyltransferase (NCBI ptt file) 176, 253
CAC2755 CAC2755 MDR-type ABC transporter (membrane associated ATPase) (NCBI ptt file) 140, 176
CAC2756 CAC2756 MDR-type ABC transporter (membrane associated ATPase) (NCBI ptt file) 102, 176
CAC2765 CAC2765 Similar to uncharacterized domain of sensory transducer protein (NCBI ptt file) 176, 309
CAC2784 CAC2784 Signal peptidase type IV (NCBI ptt file) 134, 277
CAC2786 CAC2786 Uncharacterized conserved protein, YQGV B.subtilis ortholog (NCBI ptt file) 67, 277
CAC2836 CAC2836 Zn-binding lipoprotein related (surface adhesin A), ADHS (NCBI ptt file) 52, 277
CAC3292 CAC3292 NifU homolog involved in Fe-S cluster formation (NCBI ptt file) 209, 277
CAC3360 CAC3360 Transcriptional regulator, LysR family (NCBI ptt file) 176, 277
CAC3386 CAC3386 Hypothetical protein (NCBI ptt file) 132, 176
CAC3414 CAC3414 ABC-type multidrug/protein/lipid transport system, ATPase component (NCBI ptt file) 176, 253
CAC3600 dapA Dihydrodipicolinate synthase (NCBI ptt file) 176, 277
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 CAC3360
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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