Organism : Clostridium acetobutylicum | Module List :
CAC1546 deoA

Pyrimidine-nucleoside phosphorylase (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Thymidine phosphorylase cog/ cog
pyrimidine base metabolic process go/ biological_process
thymidine phosphorylase activity go/ molecular_function
pyrimidine-nucleoside phosphorylase activity go/ molecular_function
Y_phosphoryl tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1546
(Mouseover regulator name to see its description)

CAC1546 is regulated by 18 influences and regulates 0 modules.
Regulators for CAC1546 deoA (18)
Regulator Module Operator
CAC2143 91 tf
CAC2297 91 tf
CAC2476 91 tf
CAC3166 91 tf
CAC3361 91 tf
CAC3729 91 tf
CAC0078 200 tf
CAC0183 200 tf
CAC0191 200 tf
CAC0284 200 tf
CAC0550 200 tf
CAC0681 200 tf
CAC0723 200 tf
CAC0849 200 tf
CAC1766 200 tf
CAC2052 200 tf
CAC2113 200 tf
CAC3731 200 tf

Warning: CAC1546 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
6836 7.00e-06 AGGagggg
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6837 7.90e+03 CTaGCCaCC
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7052 5.90e+02 AGgggGGattaA
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7053 2.20e+04 ctCACACAC
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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 CAC1546

CAC1546 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Thymidine phosphorylase cog/ cog
pyrimidine base metabolic process go/ biological_process
thymidine phosphorylase activity go/ molecular_function
pyrimidine-nucleoside phosphorylase activity go/ molecular_function
Y_phosphoryl tigr/ tigrfam
Module neighborhood information for CAC1546

CAC1546 has total of 42 gene neighbors in modules 91, 200
Gene neighbors (42)
Gene Common Name Description Module membership
CAC0191 CAC0191 Transcriptional regulator, RpiR family (NCBI ptt file) 200, 236
CAC0224 CAC0224 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 3, 91
CAC0229 CAC0229 Predicted Zn-dependent proteases, TLDD ortholog (NCBI ptt file) 91, 225
CAC0230 CAC0230 Inactivated predicted Zn-dependent protease, PMBA ortholog (NCBI ptt file) 91, 225
CAC0290 CAC0290 Sensory transduction histidine kinases (NCBI ptt file) 82, 91
CAC0400 CAC0400 Hypothetical protein, CF-19 family (NCBI ptt file) 91, 346
CAC0602 ftsH ATP-dependent zinc metallopeptidase FtsH (cell dividion protein) (NCBI ptt file) 91, 222
CAC0603 CAC0603 Superfamily I DNA and RNA helicase (NCBI ptt file) 91, 225
CAC0764 CAC0764 NADPH-dependent glutamate synthase beta chain (NCBI ptt file) 44, 91
CAC1035 CAC1035 Hypothetical protein (NCBI ptt file) 200, 334
CAC1246 pbpA Penicillin-binding protein 2 (NCBI ptt file) 56, 200
CAC1540 CAC1540 Uncharacterized ATP-grasp enzyme (NCBI ptt file) 71, 91
CAC1541 CAC1541 Hypothetical protein, CF-36 family (NCBI ptt file) 200, 265
CAC1544 CAC1544 Cytidine deaminase, cdd (NCBI ptt file) 91, 225
CAC1545 deoC Deoxyribose-phosphate aldolase (NCBI ptt file) 172, 200
CAC1546 deoA Pyrimidine-nucleoside phosphorylase (NCBI ptt file) 91, 200
CAC1717 CAC1717 Uncharacterized conserved protein, YLOA ortholog (NCBI ptt file) 3, 91
CAC1766 CAC1766 Predicted sigma factor (NCBI ptt file) 200, 236
CAC1796 CAC1796 Predicted membrane-associated Zn-dependent protease (NCBI ptt file) 64, 91
CAC1983 CAC1983 Hypothetical protein (NCBI ptt file) 200, 318
CAC2065 deoB Phosphopentomutase (NCBI ptt file) 51, 91
CAC2066 CAC2066 Integrase/recombinase XerD family (NCBI ptt file) 51, 91
CAC2296 CAC2296 Uncharacterized protein, YigZ family (NCBI ptt file) 3, 91
CAC2297 CAC2297 Transcriptional regulator of MocR family (DNA-binding HTH domain and aminotransferase domain) (NCBI ptt file) 3, 91
CAC2298 CAC2298 Predicted nucleotidyltransferase (NCBI ptt file) 91, 345
CAC2340 mutS1 DNA mismatch repair protein mutS, YSHD B.subtilis ortholog (NCBI ptt file) 51, 91
CAC2406 CAC2406 Predicted permease, possible O-antigen transporter (NCBI ptt file) 168, 200
CAC2415 CAC2415 Uncharacterized conserved protein (NCBI ptt file) 91, 289
CAC2433 CAC2433 HtrA-like serine protease (with PDZ domain) (NCBI ptt file) 200, 318
CAC2458 CAC2458 2-oxoacid ferredoxin oxidoreductase, beta subunit (NCBI ptt file) 41, 200
CAC2529 CAC2529 Predicted acetyltransferase (NCBI ptt file) 200, 274
CAC2531 CAC2531 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 7, 200
CAC2577 CAC2577 GGDEF domain containing protein, (inactivated) (NCBI ptt file) 168, 200
CAC2722 CAC2722 RCC1 repeats protein (beta propeller fold) (NCBI ptt file) 7, 200
CAC2736 sbcC ATPase involved in DNA repair (NCBI ptt file) 91, 98
CAC3189 clpC ATPases with chaperone activity clpC, two ATP-binding domain (NCBI ptt file) 172, 200
CAC3298 bdhB NADH-dependent butanol dehydrogenase B (BDH II) (NCBI ptt file) 172, 200
CAC3299 bdhA NADH-dependent butanol dehydrogenase A (BDH I) (NCBI ptt file) 91, 100
CAC3392 CAC3392 NADH-dependent butanol dehydrogenase (NCBI ptt file) 62, 91
CAC3571 fabZ Hydroxymyristoyl-(acyl carrier protein) dehydratase (NCBI ptt file) 65, 91
CAC3572 accB Biotin carboxyl carrier protein of acetyl-CoA carboxylase (NCBI ptt file) 44, 91
CAC3577 acp Acyl Carrier Protein, ACP (NCBI ptt file) 91, 225
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 CAC1546
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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