Organism : Clostridium acetobutylicum | Module List :
CAC2113 pyrR

Uracil phosphoribosyltransferase (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase cog/ cog
uracil phosphoribosyltransferase activity go/ molecular_function
nucleoside metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2113
(Mouseover regulator name to see its description)

CAC2113 is regulated by 20 influences and regulates 24 modules.
Regulators for CAC2113 pyrR (20)
Regulator Module Operator
CAC0265 116 tf
CAC0299 116 tf
CAC0766 116 tf
CAC0859 116 tf
CAC2053 116 tf
CAC2055 116 tf
CAC2113 116 tf
CAC3143 116 tf
CAC3149 116 tf
CAC3200 116 tf
CAC0032 160 tf
CAC0191 160 tf
CAC0681 160 tf
CAC1467 160 tf
CAC2052 160 tf
CAC2060 160 tf
CAC2084 160 tf
CAC2113 160 tf
CAC3192 160 tf
CAC3731 160 tf

Warning: CAC2113 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
6884 1.10e-01 gt.cTggGaGGtcT
Loader icon
6885 3.20e+02 AcgCcCtaCc
Loader icon
6972 1.20e+00 TgtaGGAGgag
Loader icon
6973 8.50e+03 CCcaAcCTTTTGaTTGGG
Loader icon
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 CAC2113

CAC2113 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase cog/ cog
uracil phosphoribosyltransferase activity go/ molecular_function
nucleoside metabolic process go/ biological_process
Module neighborhood information for CAC2113

CAC2113 has total of 34 gene neighbors in modules 116, 160
Gene neighbors (34)
Gene Common Name Description Module membership
CAC0025 dcd Deoxycytidine triphosphate deaminase (NCBI ptt file) 153, 160
CAC0026 CAC0026 Hypothetical protein (NCBI ptt file) 153, 160
CAC0219 CAC0219 Uracyl DNA glycosilase (NCBI ptt file) 40, 160
CAC0630 CAC0630 Peptide chain ralease factor 3 (RF-3) (NCBI ptt file) 82, 160
CAC0677 CAC0677 uncharacterized conserved protein, YdjX/UPF0043 family (NCBI ptt file) 160, 302
CAC0678 CAC0678 CBS domains (NCBI ptt file) 160, 174
CAC0765 CAC0765 Fe-S oxidoreductase (NCBI ptt file) 116, 317
CAC0766 CAC0766 Predicted transcriptional regulator (MerR family) (NCBI ptt file) 116, 360
CAC0767 CAC0767 Fe-S oxidoreductase (NCBI ptt file) 8, 116
CAC0901 CAC0901 Probably O-sialoglycoprotein endopeptidase (NCBI ptt file) 160, 233
CAC1761 CAC1761 Predicted GTPase, YLQF B.subtilis ortholog (NCBI ptt file) 116, 360
CAC1762 rnh Ribonuclease HII (NCBI ptt file) 116, 281
CAC2112 uraA Uracil permease UraA/PyrP (NCBI ptt file) 116, 160
CAC2113 pyrR Uracil phosphoribosyltransferase (NCBI ptt file) 116, 160
CAC2392 CAC2392 Uncharacterized ABC transporter, ATPase component (NCBI ptt file) 153, 160
CAC2650 pyrD Dihydroorotate dehydrogenase (NCBI ptt file) 116, 360
CAC2651 pyrZ Dihydroorotate dehydrogenase electron transfer subunit (NCBI ptt file) 30, 116
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
CAC2839 CAC2839 Inactive homolog of metal-dependent proteases. YDIC B.subtilis ortholog (NCBI ptt file) 153, 160
CAC3092 231 amidase, germination specific (cwlC/cwlD B.subtilis ortholog) (NCBI ptt file) 160, 215
CAC3093 CAC3093 Phosphate permease (NCBI ptt file) 153, 160
CAC3094 CAC3094 Uncharacterized consrved protein, associated with phosphate permease (NCBI ptt file) 153, 160
CAC3131 rplW Ribosomal protein L23 (NCBI ptt file) 116, 255
CAC3134 rpsJ Ribosomal protein S10 (NCBI ptt file) 116, 153
CAC3146 rplJ Ribosomal protein L10 (NCBI ptt file) 116, 153
CAC3148 rplK Ribosomal protein L11 (NCBI ptt file) 116, 153
CAC3149 nusG Transcription antiterminator NusG (NCBI ptt file) 116, 255
CAC3150 secE Preprotein translocase subunit SecE (NCBI ptt file) 116, 232
CAC3200 CAC3200 Predicted transcriptional regulator, homolog of Bvg accessory factor (NCBI ptt file) 76, 116
CAC3731 spoOJ Stage 0 sporulation J, ParB family of DNA-binding proteins (NCBI ptt file) 122, 160
CAC3732 gidB Glucose-inhibited division protein, GIDB (S-adenosylmethionine-dependent methyltransferase) (NCBI ptt file) 160, 254
CAC3735 jag Predicted RNA-binding protein Jag, SpoIIIJ-associated (NCBI ptt file) 160, 198
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 CAC2113
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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