Organism : Clostridium acetobutylicum | Module List :
CAC2793

Transcriptional regulator, Lrp family (possible nitrite reductase regulator NirD) (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2793
(Mouseover regulator name to see its description)

CAC2793 is regulated by 20 influences and regulates 15 modules.
Regulators for CAC2793 (20)
Regulator Module Operator
CAC0474 81 tf
CAC0549 81 tf
CAC0693 81 tf
CAC0763 81 tf
CAC0863 81 tf
CAC0865 81 tf
CAC1766 81 tf
CAC2793 81 tf
CAC3214 81 tf
CAC3438 81 tf
CAC3487 81 tf
CAC0023 203 tf
CAC0876 203 tf
CAC1430 203 tf
CAC1469 203 tf
CAC2616 203 tf
CAC2793 203 tf
CAC2794 203 tf
CAC3214 203 tf
CAC3481 203 tf

Warning: CAC2793 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
6816 1.70e-02 ggtaAaggGgGtGta
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6817 5.50e+03 GGCatCTGaC
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7058 8.70e-03 ggagGTg
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7059 1.20e+00 ataAggGaGGA
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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 CAC2793

CAC2793 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Transcriptional regulators cog/ cog
Module neighborhood information for CAC2793

CAC2793 has total of 30 gene neighbors in modules 81, 203
Gene neighbors (30)
Gene Common Name Description Module membership
CAC0613 CAC0613 Spore coat protein F (NCBI ptt file) 203, 300
CAC0614 CAC0614 Spore coat protein F (NCBI ptt file) 203, 300
CAC0742 CAC0742 Uncharacterized protein, containing predicted phosphatase domain (NCBI ptt file) 81, 127
CAC0846 CAC0846 Hypothetical protein, CF-29 family (NCBI ptt file) 81, 331
CAC0861 CAC0861 ABC-type multidrug transport system, ATPase component (NCBI ptt file) 81, 127
CAC0862 CAC0862 Transmembrane protein (NCBI ptt file) 45, 81
CAC0956 CAC0956 Hypothetical protein (NCBI ptt file) 81, 331
CAC1230 CAC1230 Hypothetical protein (NCBI ptt file) 81, 331
CAC1270 CAC1270 Hypothetical protein (NCBI ptt file) 39, 203
CAC1298 CAC1298 Uncharacterized protein, related to B.subtilis spore coat protein COTS (NCBI ptt file) 203, 330
CAC1335 CAC1335 Spore coat protein F (COTF) related protein (NCBI ptt file) 136, 203
CAC1575 CAC1575 Hypothetical protein (NCBI ptt file) 188, 203
CAC1864 CAC1864 Hypothetical protein (NCBI ptt file) 203, 290
CAC2460 CAC2460 Hypothetical protein (NCBI ptt file) 188, 203
CAC2499 CAC2499 Pyruvate ferredoxin oxidoreductase (NCBI ptt file) 188, 203
CAC2536 CAC2536 Glycosyltransferase (NCBI ptt file) 45, 81
CAC2595 CAC2595 Hypothetical protein (NCBI ptt file) 188, 203
CAC2615 CAC2615 Uncharacterized conserved protein, CotF B.subtilis family (NCBI ptt file) 135, 203
CAC2686 CAC2686 Possible maltodextrin glucosidase (NCBI ptt file) 203, 330
CAC2793 CAC2793 Transcriptional regulator, Lrp family (possible nitrite reductase regulator NirD) (NCBI ptt file) 81, 203
CAC2795 CAC2795 MoaA/NirJ family Fe-S oxidoreductase (NCBI ptt file) 81, 331
CAC2800 CAC2800 CotJC-like protein (GS80 family) (NCBI ptt file) 188, 203
CAC2801 CAC2801 TPR-repeat-containing protein, secreted (NCBI ptt file) 15, 203
CAC2985 CAC2985 Hypothetical protein (NCBI ptt file) 81, 331
CAC3002 CAC3002 Uncharacterized consrved protein, YHJR B.subtilis family (NCBI ptt file) 203, 263
CAC3081 CAC3081 Spore-cortex-lytic enzyme, SLEB (NCBI ptt file) 203, 290
CAC3218 CAC3218 Periplasmic trypsin-like serine protease (with PDZ domain), HtrA subfamily (NCBI ptt file) 81, 271
CAC3317 CAC3317 Spore coat protein F (CotF) family protein (NCBI ptt file) 188, 203
CAC3318 CAC3318 Hypothetical protein (NCBI ptt file) 45, 203
CAC3550 natB Na+ ABC transporter, NATB (NCBI ptt file) 78, 203
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 CAC2793
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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