Organism : Clostridium acetobutylicum | Module List :
CAC2859 spoIIID

Stage III sporulation protein D, SpoIIID (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
spore_III_D tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2859
(Mouseover regulator name to see its description)

CAC2859 is regulated by 17 influences and regulates 22 modules.
Regulators for CAC2859 spoIIID (17)
Regulator Module Operator
CAC0493 364 tf
CAC0723 364 tf
CAC1695 364 tf
CAC2794 364 tf
CAC2859 364 tf
CAC3214 364 tf
CAC3267 364 tf
CAC3433 364 tf
CAC3494 364 tf
CAC0197 263 tf
CAC0681 263 tf
CAC0863 263 tf
CAC1670 263 tf
CAC2616 263 tf
CAC2794 263 tf
CAC2859 263 tf
CAC3729 263 tf

Warning: CAC2859 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
7178 5.50e-03 gGAGG.t
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7179 1.20e+04 CTcCGA
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7376 2.40e+00 AtgGGaGG
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7377 2.30e+03 TAGGGC
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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 CAC2859

CAC2859 is enriched for 5 functions in 4 categories.
Enrichment Table (5)
Function System
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
spore_III_D tigr/ tigrfam
Module neighborhood information for CAC2859

CAC2859 has total of 27 gene neighbors in modules 263, 364
Gene neighbors (27)
Gene Common Name Description Module membership
CAC0579 prkA Serine protein kinase (prkA protein), P-loop containing (NCBI ptt file) 308, 364
CAC0580 CAC0580 Similar to yhbH B.subtilis (NCBI ptt file) 308, 364
CAC0581 spoVR Stage V sporulation protein R (NCBI ptt file) 308, 364
CAC0601 CAC0601 Unchracterized membrane protein, possible permease (NCBI ptt file) 263, 330
CAC1252 CAC1252 Possible membrane metalloendopeptidases (NCBI ptt file) 263, 330
CAC1673 gltA Large subunit of NADH-dependent glutamate synthase (NCBI ptt file) 263, 290
CAC2086 CAC2086 Stage III sporulation protein AH, SpoIIIAH (NCBI ptt file) 17, 364
CAC2087 CAC2087 Stage III sporulation protein AG, SpoIIIAG (NCBI ptt file) 17, 364
CAC2088 CAC2088 Stage III sporulation protein AF, SpoIIIAF (NCBI ptt file) 17, 263
CAC2089 CAC2089 Stage III sporulation protein AE, SpoIIIAE (NCBI ptt file) 263, 279
CAC2090 CAC2090 Stage III sporulation protein AD, SpoIIIAD (NCBI ptt file) 17, 263
CAC2091 CAC2091 Stage III sporulation protein AC, SpoIIIAC (NCBI ptt file) 17, 364
CAC2092 CAC2092 Stage III sporulation protein AB, SpoIIIAB (NCBI ptt file) 17, 364
CAC2093 CAC2093 Stage III sporulation protein AA, SpoIIIAA (NCBI ptt file) 17, 263
CAC2137 CAC2137 Cation transport P-type ATPase (NCBI ptt file) 17, 364
CAC2383 CAC2383 Predicted xylanase/chitin deacetylase (NCBI ptt file) 308, 364
CAC2416 CAC2416 Uncharacterized protein, ErfK family; contains peptidoglycan-binding domain (NCBI ptt file) 6, 263
CAC2426 CAC2426 Uncharacterized conserved protein (NCBI ptt file) 263, 330
CAC2427 CAC2427 Uncharacterized conserved protein (NCBI ptt file) 263, 330
CAC2428 CAC2428 Activator of 2-hydroxyglutaryl-CoA dehydratase (NCBI ptt file) 263, 330
CAC2859 spoIIID Stage III sporulation protein D, SpoIIID (NCBI ptt file) 263, 364
CAC2860 CAC2860 Hypothetical protein (NCBI ptt file) 263, 364
CAC2861 spoIID Sporulation protein SpoIID (NCBI ptt file) 263, 290
CAC2903 CAC2903 LysM domain containing membrane protein (NCBI ptt file) 263, 330
CAC2906 CAC2906 Spore coat protein cotS related (NCBI ptt file) 308, 364
CAC3002 CAC3002 Uncharacterized consrved protein, YHJR B.subtilis family (NCBI ptt file) 203, 263
CAC3278 CAC3278 Uncharacterized protein, containing cell adhesion domain and ChW-repeats (NCBI ptt file) 263, 330
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 CAC2859
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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