Organism : Clostridium acetobutylicum | Module List :
CAC2422

Oxygen-independent coproporphyrinogen III oxidase, Fe-S oxidoreductase (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Fe-S oxidoreductase cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2422
(Mouseover regulator name to see its description)

CAC2422 is regulated by 19 influences and regulates 0 modules.
Regulators for CAC2422 (19)
Regulator Module Operator
CAC0299 273 tf
CAC0402 273 tf
CAC0514 273 tf
CAC0865 273 tf
CAC0876 273 tf
CAC0929 273 tf
CAC1404 273 tf
CAC2084 273 tf
CAC3606 273 tf
CAC3695 273 tf
CAC0360 298 tf
CAC0514 298 tf
CAC0707 298 tf
CAC2053 298 tf
CAC2209 298 tf
CAC2297 298 tf
CAC2851 298 tf
CAC3199 298 tf
CAC3729 298 tf

Warning: CAC2422 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
7198 6.70e+00 AaAgcatAaaTtaagTAggGGtG
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7199 2.50e+02 AGGAggaaata
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7248 3.20e-05 aaGGa.GAtA
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7249 5.60e+03 GaGGAGGtaAGCTaG
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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 CAC2422

CAC2422 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Fe-S oxidoreductase cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
Module neighborhood information for CAC2422

CAC2422 has total of 49 gene neighbors in modules 273, 298
Gene neighbors (49)
Gene Common Name Description Module membership
CAC0005 CAC0005 Uncharacterized small conserved protein, ortholog of YAAB B.subtilis (NCBI ptt file) 64, 298
CAC0034 CAC0034 Hypothetical protein (NCBI ptt file) 63, 298
CAC0207 CAC0207 Hypothetical protein, CF-6 family (NCBI ptt file) 63, 273
CAC0277 CAC0277 HD-GYP hydrolase domain containing protein (NCBI ptt file) 109, 298
CAC0475 CAC0475 HD-GYP domain (NCBI ptt file) 107, 298
CAC0639 CAC0639 Flagellar biosynthesis related protein (NCBI ptt file) 53, 298
CAC0640 CAC0640 Predicted phoshohydrolase (NCBI ptt file) 282, 298
CAC0672 CAC0672 Fision threonyl-tRNA synthetase (N-terminal part) and uridine kinase (NCBI ptt file) 64, 273
CAC0673 CAC0673 L-serine dehydratase, beta chain (NCBI ptt file) 64, 273
CAC0904 CAC0904 ATPase with chaperon activity, two ATP-binding domains, ClpC orthologs (NCBI ptt file) 64, 298
CAC0947 CAC0947 Predicted membrane protein, hemolysin III homolog (NCBI ptt file) 38, 273
CAC0957 CAC0957 Xre family DNA-binding domain and TPR-repeat-containing protein (NCBI ptt file) 298, 348
CAC1414 CAC1414 TerE family protein, ortholog of stress responce protein SCP2 (YCEC) B.subtilis (NCBI ptt file) 272, 298
CAC1416 CAC1416 Predicted acetyltransferase (NCBI ptt file) 64, 298
CAC1485 CAC1485 Glycosyltransferase, involved in cell wall biogenesis (NCBI ptt file) 191, 298
CAC1488 CAC1488 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 63, 273
CAC1579 CAC1579 Methyl-accepting chemotaxis-like protein (chemotaxis sensory transducer) (NCBI ptt file) 90, 298
CAC1604 CAC1604 Methylglyoxal synthase (NCBI ptt file) 47, 298
CAC1605 arbA Ketopantoate reductase (NCBI ptt file) 26, 298
CAC1623 CAC1623 Uncharacterized protein, ortholog of Thermotoga (4980645) (NCBI ptt file) 210, 298
CAC1624 CAC1624 Uncharacterized protein from DegV (B.subtilis) family (NCBI ptt file) 64, 298
CAC1656 CAC1656 Hypothetical protein, CF-39 family (NCBI ptt file) 114, 273
CAC1835 miaA TRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file) 159, 273
CAC1840 CAC1840 Predicted acetyltransferase domain containing protein (NCBI ptt file) 298, 334
CAC2038 CAC2038 Hypothetical protein, CF-23 family (NCBI ptt file) 273, 312
CAC2072 CAC2072 Stage IV sporulation protein B, SpoIVB (NCBI ptt file) 63, 273
CAC2085 CAC2085 Uncharacterized protein from alkaline shock protein family, YQHY B.subtilis ortholog (NCBI ptt file) 64, 273
CAC2141 CAC2141 Hypothetical protein (NCBI ptt file) 57, 273
CAC2195 CAC2195 Protein containing aminopeptidase domain (NCBI ptt file) 298, 355
CAC2230 CAC2230 Uncharacterized protein of PR1 family, YkwD B.subtilis ortholog (NCBI ptt file) 63, 273
CAC2422 CAC2422 Oxygen-independent coproporphyrinogen III oxidase, Fe-S oxidoreductase (NCBI ptt file) 273, 298
CAC2461 CAC2461 Hypothetical protein, CF-13 family (NCBI ptt file) 264, 273
CAC2462 CAC2462 Hypothetical protein, CF-13 family (NCBI ptt file) 264, 273
CAC2631 CAC2631 Uncharacterized protein, ErfK family (NCBI ptt file) 159, 273
CAC2677 CAC2677 Lytic murein transglycosylase (NCBI ptt file) 64, 298
CAC2706 CAC2706 Uncharacterized conserved membrane protein, DedA family (NCBI ptt file) 53, 273
CAC2714 CAC2714 ABC-type transporter, duplicate ATPase component (NCBI ptt file) 157, 298
CAC2726 CAC2726 Uncharacterized protein, possible ynzC B.subtilis homolog (NCBI ptt file) 159, 298
CAC2826 CAC2826 Intracellular protease/amidase related enzyme (ThiJ family) (NCBI ptt file) 86, 273
CAC2901 CAC2901 Predicted membrane protein (NCBI ptt file) 298, 351
CAC2904 CAC2904 Uncharacterized protein, VEG B.subtilis ortholog (NCBI ptt file) 233, 298
CAC2974 CAC2974 Predicted protease from collagenase family (NCBI ptt file) 210, 273
CAC2987 CAC2987 Primase-like protein, containing TOPRIM domain, YABF B.subtilis ortholog (NCBI ptt file) 57, 273
CAC3186 CAC3186 Hypothetical protein (NCBI ptt file) 95, 273
CAC3202 ftsH ATP-dependent Zn protease, FTSH (NCBI ptt file) 273, 292
CAC3661 CAC3661 Glycosyltransferase (NCBI ptt file) 210, 273
CAC3718 CAC3718 Exopolyphosphatase-like domain and PAS domain containing protein, YYBT B.subtilis ortholog (NCBI ptt file) 182, 298
CAC3719 CAC3719 Uncharacterized predicted membrane protein, YYBS B.subtilis homolog (NCBI ptt file) 182, 298
CAC3720 CAC3720 Hypothetical protein (NCBI ptt file) 273, 298
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 CAC2422
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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