Organism : Clostridium acetobutylicum | Module List :
CAC0681 nrgB

Nitrogen regulatory protein PII, gene nrgB (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Nitrogen regulatory protein PII cog/ cog
regulation of nitrogen utilization go/ biological_process
enzyme regulator activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0681
(Mouseover regulator name to see its description)

CAC0681 is regulated by 20 influences and regulates 21 modules.
Regulators for CAC0681 nrgB (20)
Regulator Module Operator
CAC0201 235 tf
CAC0681 235 tf
CAC0768 235 tf
CAC1696 235 tf
CAC1843 235 tf
CAC3438 235 tf
CAC3443 235 tf
CAC3504 235 tf
CAC0681 367 tf
CAC0841 367 tf
CAC1509 367 tf
CAC1670 367 tf
CAC1695 367 tf
CAC2476 367 tf
CAC2568 367 tf
CAC2616 367 tf
CAC2859 367 tf
CAC3438 367 tf
CAC3651 367 tf
CAC3673 367 tf

Warning: CAC0681 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
7122 2.20e+00 gaTaAAgGtgG
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7123 2.30e+03 cAGcGGG
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7382 7.10e+03 Ag.aGGcTA
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7383 3.30e+03 CaCCTC
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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 CAC0681

CAC0681 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Nitrogen regulatory protein PII cog/ cog
regulation of nitrogen utilization go/ biological_process
enzyme regulator activity go/ molecular_function
Module neighborhood information for CAC0681

CAC0681 has total of 38 gene neighbors in modules 235, 367
Gene neighbors (38)
Gene Common Name Description Module membership
CAC0486 CAC0486 Hypothetical protein (NCBI ptt file) 73, 367
CAC0642 CAC0642 Conserved domain seen in the bacterial SpoT (NCBI ptt file) 73, 367
CAC0681 nrgB Nitrogen regulatory protein PII, gene nrgB (NCBI ptt file) 235, 367
CAC0803 CAC0803 Hypothetical protein (NCBI ptt file) 328, 367
CAC0841 CAC0841 Predicted transcriptional regulator (NCBI ptt file) 15, 367
CAC1020 CAC1020 Hypothetical protein (NCBI ptt file) 80, 367
CAC1055 CAC1055 Hypothetical protein (NCBI ptt file) 38, 367
CAC1253 CAC1253 Sporulation protein IVFB related protein, predicted metallopeptidase (NCBI ptt file) 95, 367
CAC1453 rbsB Ribose ABC transporter (ribose-binding periplasmic component) (NCBI ptt file) 235, 278
CAC1486 CAC1486 Uncharacterized protein, ortholog of YKUS B.subtilis (NCBI ptt file) 118, 367
CAC1509 CAC1509 Specialized sigma subunit of RNA polymerase (NCBI ptt file) 305, 367
CAC1551 CAC1551 Nitroreductase family protein (NCBI ptt file) 235, 248
CAC1567 CAC1567 Hypothetical protein (NCBI ptt file) 95, 367
CAC1696 sigG Specialized DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 174, 235
CAC1843 CAC1843 Predicted transcriptional regulator, YDCN B.subtilis ortholog (NCBI ptt file) 235, 280
CAC2043 CAC2043 Hypothetical protein (NCBI ptt file) 235, 366
CAC2465 CAC2465 Uncharacterized conserved protein (NCBI ptt file) 73, 367
CAC2488 CAC2488 Uncharacterized conserved protein, YTFE family (NCBI ptt file) 285, 367
CAC2802 CAC2802 Predicted phosphoglycerol transferase (alkaline phosphatase superfamily), YFNI B.subtilis (NCBI ptt file) 73, 367
CAC2838 CAC2838 Predicted nucleotide-binding protein, YjeE family (NCBI ptt file) 153, 235
CAC2840 CAC2840 Predicted acetyltransferase (NCBI ptt file) 153, 235
CAC2875 tagO Undecaprenyl-phosphate (NCBI ptt file) 174, 235
CAC2876 CAC2876 Deoxycytidylate deaminase (NCBI ptt file) 15, 367
CAC2912 araN Sugar-binding periplasmic protein (NCBI ptt file) 82, 235
CAC2913 CAC2913 Hypothetical protein (NCBI ptt file) 82, 235
CAC2914 panB Ketopantoate hydroxymethyltransferase (NCBI ptt file) 225, 235
CAC2915 panC Pantoate--beta-alanine ligase (NCBI ptt file) 235, 366
CAC2916 panD Aspartate 1-decarboxylase (NCBI ptt file) 235, 366
CAC3008 CAC3008 CBS domain containing protein (NCBI ptt file) 80, 235
CAC3019 CAC3019 Sensory transduction protein with GGDEF and EAL domains (NCBI ptt file) 73, 367
CAC3040 CAC3040 CPSC/CAPB subfamily ATPase (NCBI ptt file) 36, 235
CAC3176 ilvN Acetolactate synthase, small subunit (NCBI ptt file) 29, 367
CAC3205 spoIIE Stage II sporulation protein E, serine phosphatase family (NCBI ptt file) 42, 367
CAC3273 CAC3273 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 235, 280
CAC3393 CAC3393 Hypothetical protein (NCBI ptt file) 80, 367
CAC3504 CAC3504 Transcriptional regulator, AcrR family (NCBI ptt file) 62, 235
CAC3676 CAC3676 Uncharacterized conserved protein (NCBI ptt file) 184, 235
CAC3727 CAC3727 Uncharacterized protein, YYAC B.subtilis homolog (NCBI ptt file) 95, 367
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 CAC0681
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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