Organism : Clostridium acetobutylicum | Module List :
CAC2074 argR

Arginine repressor, argR (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Arginine repressor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
argR_whole tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2074
(Mouseover regulator name to see its description)

CAC2074 is regulated by 24 influences and regulates 22 modules.
Regulators for CAC2074 argR (24)
Regulator Module Operator
CAC0144 229 tf
CAC0514 229 tf
CAC1226 229 tf
CAC1280 229 tf
CAC1536 229 tf
CAC1719 229 tf
CAC1800 229 tf
CAC2074 229 tf
CAC2084 229 tf
CAC2568 229 tf
CAC3149 229 tf
CAC3324 229 tf
CAC0081 35 tf
CAC0144 35 tf
CAC0255 35 tf
CAC1300 35 tf
CAC1719 35 tf
CAC1799 35 tf
CAC2074 35 tf
CAC2084 35 tf
CAC2486 35 tf
CAC3200 35 tf
CAC3466 35 tf
CAC3475 35 tf

Warning: CAC2074 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
6724 3.70e-07 GGAGGaA
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6725 1.10e+03 cCtaatTttTaAGacTcaCc
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7110 2.70e-04 TtCCTcC
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7111 7.20e+01 TGgTtcctTggT.ag
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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 CAC2074

CAC2074 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Arginine repressor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
argR_whole tigr/ tigrfam
Module neighborhood information for CAC2074

CAC2074 has total of 38 gene neighbors in modules 35, 229
Gene neighbors (38)
Gene Common Name Description Module membership
CAC0508 uvrC Excinuclease ABC subunit C (NCBI ptt file) 35, 282
CAC0884 CAC0884 CAMP-binding domain (catabolite gene activator) and regulatory subunit of cAMP-dependent protein kinase (NCBI ptt file) 2, 35
CAC1090 CAC1090 5-formyltetrahydrofolate cyclo-ligase (NCBI ptt file) 159, 229
CAC1240 maf Maf protein ortholog, putative inhibitor of septum formation (NCBI ptt file) 229, 281
CAC1242 mreB mreB (NCBI ptt file) 35, 255
CAC1244 CAC1244 Predicted membrane protein (NCBI ptt file) 2, 35
CAC1293 CAC1293 Uncharacterized conserved predicted metal-binding protein, YQFG ortholog (NCBI ptt file) 51, 229
CAC1294 dgkA/pgpB Diacylglycerol kinase (dgkA) fused to phosphatase B domain (pgpB) (NCBI ptt file) 51, 229
CAC1437 CAC1437 Diverged AAA-family ATPase containing protein (NCBI ptt file) 2, 35
CAC1585 CAC1585 MDR-type permease (NCBI ptt file) 2, 35
CAC1714 ansA L-asparaginase (NCBI ptt file) 35, 350
CAC1808 pnpA Polyribonucleotide nucleotidyltransferase (NCBI ptt file) 229, 233
CAC1813 CAC1813 Predicted Fe-S oxidoreductase (NCBI ptt file) 35, 229
CAC1848 cmk Cytidylate kinase (NCBI ptt file) 35, 351
CAC2073 recN DNA repair protein recN, ATPase (NCBI ptt file) 35, 229
CAC2074 argR Arginine repressor, argR (NCBI ptt file) 35, 229
CAC2075 CAC2075 Predicted kinase (NCBI ptt file) 35, 229
CAC2076 CAC2076 Predicted rRNA methylase, YQXC B.subtilis ortholog (NCBI ptt file) 35, 229
CAC2077 CAC2077 Deoxyxylulose-5-phosphate synthase (NCBI ptt file) 159, 229
CAC2078 CAC2078 Predicted membrane protein (NCBI ptt file) 35, 229
CAC2082 xseA Exonuclease VII, large subunit (NCBI ptt file) 35, 229
CAC2126 spoVE Stage V sporulation protein E, FtsW/MrdB/SpoVE family (NCBI ptt file) 2, 229
CAC2128 murF UDP-N-acetylmuramyl pentapeptide synthase (NCBI ptt file) 2, 229
CAC2134 CAC2134 Predicted GTPase, YYAF B.subtilis ortholog (NCBI ptt file) 2, 35
CAC2282 tgt Queuine tRNA-ribosyltransferase, tgt (NCBI ptt file) 229, 234
CAC2283 queA Queuine synthetase, queA (NCBI ptt file) 35, 229
CAC2284 ruvB Holliday junction specific DNA helicase, subunit ruvB (NCBI ptt file) 26, 229
CAC2299 hflX Predicted GTPase, HflX (NCBI ptt file) 35, 304
CAC2356 pheT Phenylalanyl-tRNA synthetase (beta subunit) (NCBI ptt file) 2, 35
CAC2357 pheS Phenylalanyl-tRNA synthetase (alpha subunit) (NCBI ptt file) 2, 35
CAC2670 CAC2670 Glu-tRNAGln amidotransferase subunit A (NCBI ptt file) 79, 229
CAC2673 CAC2673 NAD-dependent DNA ligase (NCBI ptt file) 35, 315
CAC2700 guaA GMP synthase (NCBI ptt file) 35, 79
CAC2881 CAC2881 Protein-tyrosine-phosphatase, YWLE B.subtilis ortholog (NCBI ptt file) 35, 76
CAC2883 CAC2883 Predicted membrane protein (NCBI ptt file) 2, 229
CAC2884 prfA Protein chain release factor A (NCBI ptt file) 213, 229
CAC2885 CAC2885 S-adenosylmethionine-dependent methyltransferase, HEMK ortholog (NCBI ptt file) 229, 256
CAC3537 CAC3537 Fragment of SECA (fragment) (NCBI ptt file) 76, 229
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 CAC2074
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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