Organism : Clostridium acetobutylicum | Module List :
CAC3149 nusG

Transcription antiterminator NusG (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Transcription antiterminator cog/ cog
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
nusG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3149
(Mouseover regulator name to see its description)

CAC3149 is regulated by 20 influences and regulates 17 modules.
Regulators for CAC3149 nusG (20)
Regulator Module Operator
CAC0707 255 tf
CAC1799 255 tf
CAC2259 255 tf
CAC2552 255 tf
CAC3104 255 tf
CAC3142 255 tf
CAC3143 255 tf
CAC3149 255 tf
CAC3271 255 tf
CAC3677 255 tf
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

Warning: CAC3149 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
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6885 3.20e+02 AcgCcCtaCc
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7162 5.50e-01 gGAc.tG
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7163 4.30e+02 AgGagGataat
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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 CAC3149

CAC3149 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcription antiterminator cog/ cog
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
nusG tigr/ tigrfam
Module neighborhood information for CAC3149

CAC3149 has total of 40 gene neighbors in modules 116, 255
Gene neighbors (40)
Gene Common Name Description Module membership
CAC0748 CAC0748 Nitroreductase family protein (NCBI ptt file) 154, 255
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
CAC1242 mreB mreB (NCBI ptt file) 35, 255
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
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
CAC2710 etfB Electron transfer flavoprotein beta-subunit (NCBI ptt file) 255, 259
CAC2711 bcd Butyryl-CoA dehydrogenase (NCBI ptt file) 232, 255
CAC3004 folA Dihydrofolate reductase (NCBI ptt file) 255, 258
CAC3087 CAC3087 Phosphoenolpyruvate-protein kinase (PTS system enzyme I) (NCBI ptt file) 4, 255
CAC3099 truA Pseudouridylate synthase, TRUA (NCBI ptt file) 106, 255
CAC3101 CAC3101 ABC-type transporter, ATPase component (cobalt transporters subfamily) (NCBI ptt file) 79, 255
CAC3102 CAC3102 ABC-type transporter, ATPase component (cobalt transporters subfamily) (NCBI ptt file) 255, 358
CAC3107 rpsM Ribosomal protein S13 (NCBI ptt file) 255, 358
CAC3109 infA Translation initiation factor IF-1 (NCBI ptt file) 255, 292
CAC3110 CAC3110 Ribosomal protein L14E (archaeal/eukaryotic type) (NCBI ptt file) 255, 358
CAC3118 rplF Ribosomal protein L6 (NCBI ptt file) 255, 358
CAC3122 rplX Ribosomal protein L24 (NCBI ptt file) 255, 304
CAC3125 rpmC Ribosomal protein L29 (NCBI ptt file) 255, 358
CAC3129 rpsS Ribosomal protein S19 (NCBI ptt file) 237, 255
CAC3131 rplW Ribosomal protein L23 (NCBI ptt file) 116, 255
CAC3133 rplC Ribosomal protein L3 (NCBI ptt file) 254, 255
CAC3134 rpsJ Ribosomal protein S10 (NCBI ptt file) 116, 153
CAC3142 rpoC DNA-dependent RNA polymerase beta' subunit (NCBI ptt file) 255, 335
CAC3143 rpoB DNA-dependent RNA polymerase beta subunit (NCBI ptt file) 255, 335
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
CAC3151 rpmG L33 (NCBI ptt file) 5, 255
CAC3200 CAC3200 Predicted transcriptional regulator, homolog of Bvg accessory factor (NCBI ptt file) 76, 116
CAC3222 gcaD UDP-N-acetylglucosamine pyrophosphorylase (NCBI ptt file) 255, 312
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 CAC3149
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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