Organism : Clostridium acetobutylicum | Module List :
CAC1396 purD

Phosphoribosylamine-glycine ligase (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Phosphoribosylamine-glycine ligase cog/ cog
phosphoribosylamine-glycine ligase activity go/ molecular_function
ATP binding go/ molecular_function
purine base biosynthetic process go/ biological_process
purD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1396
(Mouseover regulator name to see its description)

CAC1396 is regulated by 18 influences and regulates 0 modules.
Regulators for CAC1396 purD (18)
Regulator Module Operator
CAC0459 249 tf
CAC0559 249 tf
CAC1226 249 tf
CAC1509 249 tf
CAC2773 249 tf
CAC3271 249 tf
CAC3283 249 tf
CAC3418 249 tf
CAC3466 249 tf
CAC0078 360 tf
CAC0571 360 tf
CAC0766 360 tf
CAC1320 360 tf
CAC1451 360 tf
CAC1799 360 tf
CAC2052 360 tf
CAC2113 360 tf
CAC3199 360 tf

Warning: CAC1396 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
7150 1.30e-02 gGAGGaA
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7151 1.80e+02 gGGcGG
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7370 8.90e-09 GGAGGtA
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7371 6.30e+03 GGCacGTG
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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 CAC1396

CAC1396 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Phosphoribosylamine-glycine ligase cog/ cog
phosphoribosylamine-glycine ligase activity go/ molecular_function
ATP binding go/ molecular_function
purine base biosynthetic process go/ biological_process
purD tigr/ tigrfam
Module neighborhood information for CAC1396

CAC1396 has total of 43 gene neighbors in modules 249, 360
Gene neighbors (43)
Gene Common Name Description Module membership
CAC0414 CAC0414 Hypothetical protein (NCBI ptt file) 211, 249
CAC0423 CAC0423 Fusion: PTS system, beta-glucosides specific IIABC component (NCBI ptt file) 284, 360
CAC0425 sacA Sucrase-6-phosphate hydrolase (gene sacA) (NCBI ptt file) 92, 360
CAC0528 CAC0528 ABC transporter, ATPase component (two ATPase domains) (NCBI ptt file) 249, 281
CAC0570 CAC0570 PTS enzyme II, ABC component (NCBI ptt file) 237, 360
CAC0586 CAC0586 CheX protein (uncharacterized ORF in chemotaxis operon) (NCBI ptt file) 70, 249
CAC0644 gerKA Spore germination protein gerKA (NCBI ptt file) 324, 360
CAC0766 CAC0766 Predicted transcriptional regulator (MerR family) (NCBI ptt file) 116, 360
CAC1146 CAC1146 Hypothetical protein (NCBI ptt file) 16, 249
CAC1149 CAC1149 Hypothetical protein (NCBI ptt file) 16, 249
CAC1150 CAC1150 Hypothetical protein (NCBI ptt file) 16, 249
CAC1153 CAC1153 Hypothetical protein (NCBI ptt file) 16, 249
CAC1155 CAC1155 Hypothetical protein (NCBI ptt file) 16, 249
CAC1157 CAC1157 Hypothetical protein (NCBI ptt file) 16, 249
CAC1159 CAC1159 Hypothetical protein (NCBI ptt file) 16, 249
CAC1392 purF Glutamine phosphoribosylpyrophosphate amidotransferase (NCBI ptt file) 193, 249
CAC1395 purH AICAR transformylase/IMP cyclohydrolase (NCBI ptt file) 193, 249
CAC1396 purD Phosphoribosylamine-glycine ligase (NCBI ptt file) 249, 360
CAC1590 CAC1590 2-oxoglutarate/malate translocator (NCBI ptt file) 66, 249
CAC1595 CAC1595 Integrase/recombinase, XerC/XerD family (NCBI ptt file) 249, 360
CAC1613 CAC1613 ABC-type multidrug/protein/lipid transport system, membrane ATPase component (NCBI ptt file) 76, 249
CAC1630 CAC1630 Zn-dependent peptidase from MPP family (NCBI ptt file) 22, 360
CAC1655 purQ/purL bifunctional enzyme phosphoribosylformylglycinamidine (FGAM) synthase (synthetase domain/glutamine amidotransferase domain) (NCBI ptt file) 214, 249
CAC1761 CAC1761 Predicted GTPase, YLQF B.subtilis ortholog (NCBI ptt file) 116, 360
CAC1789 smbA/pyrH Uridylate kinase (NCBI ptt file) 310, 360
CAC2617 CAC2617 Membrane associated methyl-chemotaxis protein, HAMP domain containing (NCBI ptt file) 66, 360
CAC2626 fabG Possible 3-ketoacyl-acyl carrier protein reductase (NCBI ptt file) 310, 360
CAC2627 CAC2627 Predicted S-adenosylmethionine-dependent methyltransferase, YtmQ B.subtilis ortholog (NCBI ptt file) 310, 360
CAC2628 CAC2628 Predicted metal-dependent peptidase (NCBI ptt file) 310, 360
CAC2650 pyrD Dihydroorotate dehydrogenase (NCBI ptt file) 116, 360
CAC2652 pyrF Orotidine-5'-phosphate decarboxylase (NCBI ptt file) 116, 360
CAC2653 pyrI Aspartate carbamoyltransferase regulatory subunit (NCBI ptt file) 116, 360
CAC2654 CAC2654 Aspartate carbamoyltransferase catalytic subunit (NCBI ptt file) 116, 360
CAC2918 pmi Mannose-6 phospate isomelase (NCBI ptt file) 270, 360
CAC2936 CAC2936 Alpha/beta superfamily hydrolase (NCBI ptt file) 236, 360
CAC3095 thiK Hydroxyethylthiazole kinase ThiM/ThiK (FS!) (NCBI ptt file) 353, 360
CAC3332 CAC3332 Predicted amidohydrolase (dihydroorothase family) (NCBI ptt file) 150, 360
CAC3356 CAC3356 Lactoylglutathione lyase (LGUL) family protein, diverged (NCBI ptt file) 236, 360
CAC3440 CAC3440 Hypothetical protein (NCBI ptt file) 353, 360
CAC3527 CAC3527 Ferredoxin (NCBI ptt file) 66, 249
CAC3622 CAC3622 Possible subunit of benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase (NCBI ptt file) 193, 249
CAC3625 CAC3625 Fe-S oxidoreductase of MoaA family (NCBI ptt file) 193, 249
CAC3626 mtrA GTP cyclohydrolase I (NCBI ptt file) 193, 249
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 CAC1396
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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