Organism : Clostridium acetobutylicum | Module List :
CAC3224 purR

PUR operon repressor, Adenine/guanine phosphoribosyltransferase family (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins cog/ cog
DNA binding go/ molecular_function
nucleoside metabolic process go/ biological_process
transcription repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
negative regulation of purine base metabolic process go/ biological_process
purR_Bsub tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3224
(Mouseover regulator name to see its description)

CAC3224 is regulated by 19 influences and regulates 9 modules.
Regulators for CAC3224 purR (19)
Regulator Module Operator
CAC0115 232 tf
CAC0493 232 tf
CAC2222 232 tf
CAC3037 232 tf
CAC3579 232 tf
CAC3647 232 tf
CAC0019 292 tf
CAC0078 292 tf
CAC0115 292 tf
CAC0474 292 tf
CAC1046 292 tf
CAC1086 292 tf
CAC1588 292 tf
CAC1945 292 tf
CAC1965 292 tf
CAC2071 292 tf
CAC3104 292 tf
CAC3224 292 tf
CAC3418 292 tf
Regulated by CAC3224 (9)
Module Residual Genes
30 0.33 20
75 0.34 19
219 0.33 19
228 0.31 16
233 0.41 16
239 0.43 21
286 0.45 25
292 0.41 24
306 0.38 20
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7116 7.50e-02 agGaGgtggag
Loader icon
7117 1.90e+03 GCCCGT
Loader icon
7236 3.10e-03 GGaGgG
Loader icon
7237 6.90e+03 cGcCACAaGG
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 CAC3224

CAC3224 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins cog/ cog
DNA binding go/ molecular_function
nucleoside metabolic process go/ biological_process
transcription repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
negative regulation of purine base metabolic process go/ biological_process
purR_Bsub tigr/ tigrfam
Module neighborhood information for CAC3224

CAC3224 has total of 39 gene neighbors in modules 232, 292
Gene neighbors (39)
Gene Common Name Description Module membership
CAC0082 CAC0082 Predicted membrane protein (NCBI ptt file) 178, 292
CAC0115 CAC0115 Uncharacterized protein, Yje/RRF2 family (NCBI ptt file) 63, 232
CAC0217 pheA Prephenate dehydrotase (pheA) (NCBI ptt file) 182, 292
CAC0322 CAC0322 Sensory protein, containing EAL-domain (NCBI ptt file) 232, 295
CAC0476 pepT Peptidase T (aminotripeptidase), gene pepT (NCBI ptt file) 286, 292
CAC0493 CAC0493 Uncharcterized small conserved protein, YhhG family (NCBI ptt file) 64, 232
CAC0494 CAC0494 PemK family of DNA-binding proteins (NCBI ptt file) 32, 232
CAC0651 CAC0651 Hypothetical protein (NCBI ptt file) 292, 352
CAC0711 tpi Triosephosphate isomerase (NCBI ptt file) 128, 292
CAC0712 pgm 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gene (NCBI ptt file) 20, 292
CAC0944 tkt Transketolase (NCBI ptt file) 84, 292
CAC1289 CAC1289 Uncharacterized conserved protein, YqeY B.subtilis ortholog (NCBI ptt file) 32, 232
CAC1356 thiH Thiamine biosynthesis enzyme ThiH (NCBI ptt file) 196, 292
CAC1386 CAC1386 Zn-dependent hydrolases, glyoxylase family (NCBI ptt file) 182, 292
CAC1745 rpmF Ribosomal protein L32 (NCBI ptt file) 32, 232
CAC1747 acpA Acyl carrier protein, ACP (NCBI ptt file) 32, 232
CAC2286 CAC2286 Uncharacterized protein, similar to protein from Clostridium histolyticum (GI:3892648) (NCBI ptt file) 292, 352
CAC2484 CAC2484 Predicted membrane, YQJA B.subtilis ortholog (NCBI ptt file) 47, 292
CAC2711 bcd Butyryl-CoA dehydrogenase (NCBI ptt file) 232, 255
CAC2712 crt Crotonase (3-hydroxybutyryl-COA dehydratase) (NCBI ptt file) 61, 232
CAC2856 metK S-adenosylmethionine synthetase (NCBI ptt file) 32, 232
CAC3023 CAC3023 Hypothetical protein (NCBI ptt file) 268, 292
CAC3109 infA Translation initiation factor IF-1 (NCBI ptt file) 255, 292
CAC3113 seqY Preprotein translocase subunit SecY (NCBI ptt file) 292, 304
CAC3135 CAC3135 Uncharacterized C4-type Zn-finger containing protein (NCBI ptt file) 232, 237
CAC3145 rplL Ribosomal protein L7/L12 (NCBI ptt file) 61, 232
CAC3147 rplA Ribosomal protein L1 (NCBI ptt file) 61, 232
CAC3150 secE Preprotein translocase subunit SecE (NCBI ptt file) 116, 232
CAC3175 CAC3175 Hypothetical protein (NCBI ptt file) 73, 292
CAC3201 CAC3201 Formate--tetrahydrofolate ligase (NCBI ptt file) 201, 292
CAC3202 ftsH ATP-dependent Zn protease, FTSH (NCBI ptt file) 273, 292
CAC3224 purR PUR operon repressor, Adenine/guanine phosphoribosyltransferase family (NCBI ptt file) 232, 292
CAC3225 murC UDP-N-acetylmuramate-alanine ligase (NCBI ptt file) 292, 359
CAC3252 proC Pyrroline-5-carboxylate reductase (NCBI ptt file) 85, 232
CAC3260 asnS Aspartyl/asparaginyl-tRNA synthetase (NCBI ptt file) 82, 292
CAC3376 CAC3376 Possible pectin degradation protein (sugar phosphate isomerase family) (NCBI ptt file) 113, 292
CAC3394 CAC3394 Uncharacterized conserved protein, YGIN family (NCBI ptt file) 232, 292
CAC3595 CAC3595 Uncharacterized FAD-dependent dehydrogenase (NCBI ptt file) 182, 292
CAC3695 CAC3695 Possible transcriptional regulator, containing DNA-binding domain of xre family (NCBI ptt file) 113, 292
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 CAC3224
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