Organism : Clostridium acetobutylicum | Module List :
CAC3199

NifR3 family enzyme (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
tRNA-dihydrouridine synthase cog/ cog
tRNA processing go/ biological_process
oxidoreductase activity go/ molecular_function
flavin adenine dinucleotide binding go/ molecular_function
nifR3_yhdG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3199
(Mouseover regulator name to see its description)

CAC3199 is regulated by 17 influences and regulates 16 modules.
Regulators for CAC3199 (17)
Regulator Module Operator
CAC0627 256 tf
CAC1032 256 tf
CAC1300 256 tf
CAC1675 256 tf
CAC1766 256 tf
CAC1800 256 tf
CAC1950 256 tf
CAC2634 256 tf
CAC3166 256 tf
CAC3199 256 tf
CAC3669 256 tf
CAC0461 79 tf
CAC0933 79 tf
CAC1719 79 tf
CAC3199 79 tf
CAC3429 79 tf
CAC3646 79 tf

Warning: CAC3199 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
6812 4.20e+02 cgAGGtG
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6813 3.80e+04 CAGaCCAAacG
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7164 6.00e-01 gGaGtGc
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7165 1.20e+04 GgCAaAGG
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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 CAC3199

CAC3199 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
tRNA-dihydrouridine synthase cog/ cog
tRNA processing go/ biological_process
oxidoreductase activity go/ molecular_function
flavin adenine dinucleotide binding go/ molecular_function
nifR3_yhdG tigr/ tigrfam
Module neighborhood information for CAC3199

CAC3199 has total of 46 gene neighbors in modules 79, 256
Gene neighbors (46)
Gene Common Name Description Module membership
CAC0018 CAC0018 Putative NADPH-quinone reductase, YabF family (NCBI ptt file) 256, 327
CAC0365 CAC0365 Phosphoglycerate dehydrogenase (NCBI ptt file) 256, 316
CAC0367 rocB Arginine degradation protein (gene rocB) (NCBI ptt file) 256, 271
CAC0376 CAC0376 N-dimethylarginine dimethylaminohydrolase (similar to ykgA B.subtilis) (NCBI ptt file) 111, 256
CAC0377 CAC0377 Amino acid (glutamine) ABC transporter, permease component (NCBI ptt file) 172, 256
CAC0460 CAC0460 CBS-domain containing protein, YHDP B.subtilis ortholog (NCBI ptt file) 79, 172
CAC0461 CAC0461 Mercuric resistance operon regulatory protein, MerR family (NCBI ptt file) 79, 224
CAC0574 CAC0574 Pectate lyase H (FS) (NCBI ptt file) 123, 256
CAC0638 CAC0638 Hypothetical protein (NCBI ptt file) 79, 120
CAC0649 CAC0649 Uncharacterized protein, homolog of Thermotoga maritima (4982386) (NCBI ptt file) 79, 172
CAC0710 pgk 3-phosphoglycerate kinase (NCBI ptt file) 79, 335
CAC0962 CAC0962 UDP-N-acetylmuramyl tripeptide synthetase (NCBI ptt file) 79, 151
CAC0998 CAC0998 Homoserine dehydrogenase (NCBI ptt file) 234, 256
CAC0999 thrC Threonine synthase (NCBI ptt file) 234, 256
CAC1000 CAC1000 Uncharacterized protein, homolog of yhfF B.subtilis (NCBI ptt file) 256, 327
CAC1260 obg SPO0B-associated GTPase, obg (NCBI ptt file) 172, 256
CAC1261 CAC1261 Predicted RNA-binding protein containing KH domain (NCBI ptt file) 172, 256
CAC1300 sigA RNA polymerase sigma factor RPOD (NCBI ptt file) 159, 256
CAC1352 CAC1352 Membrane associated chemotaxis sensory transducer protein (MSP domain and HAMP domain) (NCBI ptt file) 137, 256
CAC1408 CAC1408 Phospho-beta-glucosidase (NCBI ptt file) 79, 343
CAC1427 gabT 4-aminobutyrate aminotransferase (PLP-dependent) (NCBI ptt file) 111, 256
CAC1501 CAC1501 DNA-methyltransferase (cytosine-specific), ortholog of BSP6I Bsubtilis (NCBI ptt file) 76, 79
CAC1785 topA Topoisomerase I (NCBI ptt file) 79, 281
CAC2105 CAC2105 General secretion pathway protein E, ATPase (NCBI ptt file) 256, 320
CAC2190 spsF Spore coat polysaccharide biosynthesis protein F (NCBI ptt file) 79, 120
CAC2246 CAC2246 Lysophospholipase L2 PLDB, hydrolase of alpha/beta superfamily (NCBI ptt file) 28, 79
CAC2351 CAC2351 Glycosyltransferase (NCBI ptt file) 100, 256
CAC2368 CAC2368 Hypothetical protein (NCBI ptt file) 254, 256
CAC2669 CAC2669 Glu-tRNAGln amidotransferase subunit B (NCBI ptt file) 79, 332
CAC2670 CAC2670 Glu-tRNAGln amidotransferase subunit A (NCBI ptt file) 79, 229
CAC2671 CAC2671 Glu-tRNAGln amidotransferase subunit C (NCBI ptt file) 79, 281
CAC2700 guaA GMP synthase (NCBI ptt file) 35, 79
CAC2758 CAC2758 Uncharacterized protein, YPUA B.subtilis ortholog (NCBI ptt file) 79, 172
CAC2869 atpF FoF1-type ATP synthase B subunit (NCBI ptt file) 79, 335
CAC2871 atpB FoF1-type ATP synthase A subunit (NCBI ptt file) 59, 79
CAC2882 CAC2882 Predicted translation factor (SUA5) (NCBI ptt file) 79, 256
CAC2885 CAC2885 S-adenosylmethionine-dependent methyltransferase, HEMK ortholog (NCBI ptt file) 229, 256
CAC2886 CAC2886 Uncharacterized conserved protein, predicted metal-dependent enzyme, YQHQ B.subtilis ortholog (NCBI ptt file) 79, 256
CAC2948 CAC2948 ATPase components of ABC transporter with duplicated ATPase domains (second domain is inactivated) (NCBI ptt file) 79, 84
CAC2989 CAC2989 PHP superfamily hydrolase, YABD ortholog (NCBI ptt file) 254, 256
CAC3039 CAC3039 Hypothetical secreted protein (NCBI ptt file) 245, 256
CAC3090 CAC3090 Fumarate hydratase, subunit B (C-terminal domain of FumA E.coli) class I (NCBI ptt file) 10, 79
CAC3096 thiK Hydroxyethylthiazole kinase ThiM/ThiK (FS!) (NCBI ptt file) 256, 316
CAC3101 CAC3101 ABC-type transporter, ATPase component (cobalt transporters subfamily) (NCBI ptt file) 79, 255
CAC3199 CAC3199 NifR3 family enzyme (NCBI ptt file) 79, 256
CAC3586 cinA Competence-damage inducible protein, CINA (NCBI ptt file) 79, 100
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 CAC3199
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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