Organism : Clostridium acetobutylicum | Module List :
CAC3343

Biotin synthase related domain containing protein (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Predicted DNA-binding protein with the Helix-hairpin-helix motif cog/ cog
catalytic activity go/ molecular_function
intracellular go/ cellular_component
metabolic process go/ biological_process
sequence-specific DNA binding go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
rSAM_link_UDG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3343
(Mouseover regulator name to see its description)

CAC3343 is regulated by 19 influences and regulates 0 modules.
Regulators for CAC3343 (19)
Regulator Module Operator
CAC0189 9 tf
CAC0289 9 tf
CAC1264 9 tf
CAC1467 9 tf
CAC2242 9 tf
CAC2306 9 tf
CAC3283 9 tf
CAC3424 9 tf
CAC3525 9 tf
CAC0183 236 tf
CAC0191 236 tf
CAC1463 236 tf
CAC1467 236 tf
CAC1668 236 tf
CAC1753 236 tf
CAC2471 236 tf
CAC3037 236 tf
CAC3507 236 tf
CAC3651 236 tf

Warning: CAC3343 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
6672 6.80e-04 tGGaGG
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6673 3.70e+03 GTGCcTACTTG
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7124 2.20e+02 gGAGGT
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7125 1.10e+03 AAggGtGGAT
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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 CAC3343

CAC3343 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Predicted DNA-binding protein with the Helix-hairpin-helix motif cog/ cog
catalytic activity go/ molecular_function
intracellular go/ cellular_component
metabolic process go/ biological_process
sequence-specific DNA binding go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
rSAM_link_UDG tigr/ tigrfam
Module neighborhood information for CAC3343

CAC3343 has total of 36 gene neighbors in modules 9, 236
Gene neighbors (36)
Gene Common Name Description Module membership
CAC0035 CAC0035 Serine/threonine phosphatase (inactivated protein) (NCBI ptt file) 236, 353
CAC0182 CAC0182 Beta-glucosidase homolog (NCBI ptt file) 236, 320
CAC0184 CAC0184 Predicted acetyltransferase (NCBI ptt file) 236, 314
CAC0191 CAC0191 Transcriptional regulator, RpiR family (NCBI ptt file) 200, 236
CAC0430 CAC0430 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 165, 236
CAC0582 CAC0582 Cobyrinic acid a,c-diamide synthase CobB/CbiA (CBIB protein) (NCBI ptt file) 236, 288
CAC0699 CAC0699 Spore photoproduct lyase, splB (NCBI ptt file) 9, 217
CAC0786 CAC0786 Uncharacterized conserved protein, repeats (NCBI ptt file) 154, 236
CAC0799 psd Phosphatidylserine decarboxylase (NCBI ptt file) 183, 236
CAC1054 CAC1054 Arginase (NCBI ptt file) 165, 236
CAC1466 CAC1466 Hypothetical protein (NCBI ptt file) 39, 236
CAC1570 bsaA Glutathione peroxidase (NCBI ptt file) 9, 70
CAC1601 CAC1601 Methyl-accepting chemotaxis-like protein (chemotaxis sensory transducer) (NCBI ptt file) 9, 299
CAC1766 CAC1766 Predicted sigma factor (NCBI ptt file) 200, 236
CAC2526 CAC2526 6-pyruvoyl-tetrahydropterin synthase related protein (NCBI ptt file) 9, 191
CAC2619 CAC2619 Acyl-CoA thioesterase family protein (NCBI ptt file) 9, 96
CAC2745 CAC2745 Membrane associated methyl-accepting chemotaxis protein (NCBI ptt file) 208, 236
CAC2933 CAC2933 Ferredoxin-like domain fused to nitroreductase-like domain (NCBI ptt file) 9, 92
CAC2936 CAC2936 Alpha/beta superfamily hydrolase (NCBI ptt file) 236, 360
CAC3044 CAC3044 CPSD/CAPA conserved membrane protein of Rol/Cld family (NCBI ptt file) 9, 48
CAC3053 CAC3053 Histidinol phosphatase related enzyme (NCBI ptt file) 9, 323
CAC3056 CAC3056 Nucleoside-diphosphate-sugar pyrophosphorylase (NCBI ptt file) 9, 323
CAC3058 CAC3058 Mannose-1-phosphate guanylyltransferase (NCBI ptt file) 9, 323
CAC3059 CAC3059 Sugar transferases (NCBI ptt file) 9, 48
CAC3282 CAC3282 ABC-type multidrug/protein/lipid transport system, ATPase component (NCBI ptt file) 9, 324
CAC3283 CAC3283 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 9, 324
CAC3343 CAC3343 Biotin synthase related domain containing protein (NCBI ptt file) 9, 236
CAC3344 CAC3344 Uncharacterized protein, homolog of hypothetical protein (GI:5918205) from Pseudomonas stutzeri (NCBI ptt file) 165, 236
CAC3356 CAC3356 Lactoylglutathione lyase (LGUL) family protein, diverged (NCBI ptt file) 236, 360
CAC3445 CAC3445 Predicted acetyltransferase (NCBI ptt file) 9, 224
CAC3459 CAC3459 Homolog of cell division GTPase FtsZ, diverged (NCBI ptt file) 9, 242
CAC3507 CAC3507 Transcriptional regulator, MerR family (NCBI ptt file) 236, 265
CAC3604 ilvD Dihydroxyacid dehydratase (NCBI ptt file) 236, 288
CAC3605 gntP High affinity gluconate/L-idonate permease (NCBI ptt file) 236, 288
CAC3688 CAC3688 Membrane-associated methyl-accepting chemotaxis protein with HAMP domain (NCBI ptt file) 165, 236
CAC3726 CAC3726 Uncharacterized conserved membrane protein, YjeP/UPF0003 family (NCBI ptt file) 9, 165
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 CAC3343
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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