Organism : Clostridium acetobutylicum | Module List :
CAC0590 ribD

Riboflavin biosynthesis protein RIBD (pirimidine deaminase and pirimidine reductase) (NCBI ptt file)

CircVis
Functional Annotations (10)
Function System
Pyrimidine reductase, riboflavin biosynthesis cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
5-amino-6-(5-phosphoribosylamino)uracil reductase activity go/ molecular_function
diaminohydroxyphosphoribosylaminopyrimidine deaminase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
NADP binding go/ molecular_function
ribD_Cterm tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0590
(Mouseover regulator name to see its description)

CAC0590 is regulated by 21 influences and regulates 0 modules.
Regulators for CAC0590 ribD (21)
Regulator Module Operator
CAC0078 291 tf
CAC0144 291 tf
CAC0240 291 tf
CAC0284 291 tf
CAC0559 291 tf
CAC0599 291 tf
CAC1046 291 tf
CAC1355 291 tf
CAC2471 291 tf
CAC2473 291 tf
CAC2818 291 tf
CAC3349 291 tf
CAC3525 291 tf
CAC3579 291 tf
CAC3646 291 tf
CAC0023 266 tf
CAC0933 266 tf
CAC1032 266 tf
CAC3143 266 tf
CAC3502 266 tf
CAC3695 266 tf

Warning: CAC0590 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
7184 4.50e-01 TccggaGCCgaCAGT
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7185 2.90e+03 GTCTGGATGAAAGAAG
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7234 8.90e+02 ggggcCGAc.g
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7235 2.70e-01 AggaGG
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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 CAC0590

CAC0590 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Pyrimidine reductase, riboflavin biosynthesis cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
5-amino-6-(5-phosphoribosylamino)uracil reductase activity go/ molecular_function
diaminohydroxyphosphoribosylaminopyrimidine deaminase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
NADP binding go/ molecular_function
ribD_Cterm tigr/ tigrfam
Module neighborhood information for CAC0590

CAC0590 has total of 43 gene neighbors in modules 266, 291
Gene neighbors (43)
Gene Common Name Description Module membership
CAC0023 CAC0023 Transcriptional regulator, LysR family (NCBI ptt file) 179, 266
CAC0286 CAC0286 Uncharacterized membrane protein (NCBI ptt file) 218, 266
CAC0287 CAC0287 Uncharacterized membrane protein (NCBI ptt file) 218, 266
CAC0288 CAC0288 ABC transporter, ATP-binding protein (NCBI ptt file) 67, 266
CAC0511 CAC0511 Predicted P-loop containing kinase, similar to B.subtilis yvcJ (NCBI ptt file) 102, 291
CAC0535 CAC0535 Metal-dependent hydrolase of the beta-lactamase superfamily II (NCBI ptt file) 47, 291
CAC0567 CAC0567 Putative methyltransferase (NCBI ptt file) 33, 266
CAC0587 CAC0587 Flavodoxin (NCBI ptt file) 214, 266
CAC0588 CAC0588 Hypothetical protein (NCBI ptt file) 227, 266
CAC0590 ribD Riboflavin biosynthesis protein RIBD (pirimidine deaminase and pirimidine reductase) (NCBI ptt file) 266, 291
CAC0591 ribB Riboflavin synthase alpha chain (NCBI ptt file) 221, 291
CAC0592 ribA Riboflavin biosynthes protein RIBA (GTPcyclohydrolase/3,4-dihydroxy-2-butanone 4-phosphate synthase) (NCBI ptt file) 221, 291
CAC0593 ribH Riboflavin synthase beta-chain (NCBI ptt file) 221, 291
CAC0594 CAC0594 Predicted phosphate-utilizing enzyme involved in pyridoxine/purine/histidine biosynthesis (NCBI ptt file) 83, 266
CAC0595 CAC0595 Glutamine amidotranspherase (possibly involved in histidine and purine biosinthesis) (NCBI ptt file) 83, 291
CAC0599 CAC0599 Transcriptional regulator, GntR family (NCBI ptt file) 223, 291
CAC0625 CAC0625 Possible periplasmic aspartyl protease (NCBI ptt file) 24, 266
CAC0669 CAC0669 Hypothetical protein (NCBI ptt file) 83, 266
CAC0749 CAC0749 HD hydrolase superfamily protein (NCBI ptt file) 154, 291
CAC0982 CAC0982 Hypothetical protein (NCBI ptt file) 209, 266
CAC1030 CAC1030 FeoA-like protein, involved in iron transport (NCBI ptt file) 83, 266
CAC1039 CAC1039 Membrane protein, TerC homolog (NCBI ptt file) 11, 266
CAC1549 bsaA Glutathione peroxidase (NCBI ptt file) 83, 266
CAC1636 CAC1636 Uncharacterized protein, homolog of B. firmus (2654481) (NCBI ptt file) 291, 349
CAC1638 CAC1638 Hypothetical protein, CF-37 family(almost identical) (NCBI ptt file) 291, 349
CAC1639 CAC1639 Hypothetical protein, CF-7 family (NCBI ptt file) 291, 349
CAC1640 CAC1640 Uncharacterized protein, YQCG B.subtilis homolog; CF-7 family (NCBI ptt file) 291, 349
CAC1671 CAC1671 Predicted ATPase related to the helicase subunit of the Holliday junction resolvase (NCBI ptt file) 291, 326
CAC1672 CAC1672 Rad3-related DNA helicase (NCBI ptt file) 291, 326
CAC1966 CAC1966 Surface-layer related glycoprotein (NCBI ptt file) 70, 291
CAC1969 CAC1969 Possible plasmid transfer factor, TraK (NCBI ptt file) 287, 291
CAC2541 CAC2541 Reductase/isomerase/elongation factor common domain (NCBI ptt file) 70, 291
CAC2544 etfB Electron-transferring flavoprotein small subunit (NCBI ptt file) 41, 291
CAC2692 CAC2692 O-Acetyltransferase, from isoleucine patch superfamily (NCBI ptt file) 70, 266
CAC2841 CAC2841 Conserved membrane protein, probable transporter, YPAA B.subtilis ortholog (NCBI ptt file) 262, 266
CAC3020 CAC3020 Ornithine acetyltransferase/N-acetylglutamate synthase (NCBI ptt file) 266, 321
CAC3181 CAC3181 Oligopeptide ABC transporter, permease component (NCBI ptt file) 266, 321
CAC3350 CAC3350 Putative intracellular protease/amidase (ThiJ family) (NCBI ptt file) 230, 291
CAC3354 CAC3354 Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file) 206, 266
CAC3359 CAC3359 Nitroreductase family protein fused to ferredoxin domain (NCBI ptt file) 86, 266
CAC3505 CAC3505 Multimeric flavodoxin WrbA family protein (NCBI ptt file) 212, 291
CAC3576 CAC3576 Dioxygenase related to 2-nitropropane dioxygenase (NCBI ptt file) 6, 291
CAC3656 CAC3656 Uncharacterized conserved protein, yaiN/yohL family (NCBI ptt file) 185, 291
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 CAC0590
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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