Organism : Clostridium acetobutylicum | Module List :
CAC2535

Predicted protein of beta-propeller fold (NCBI ptt file)

CircVis
Functional Annotations (9)
Function System
Uncharacterized conserved protein cog/ cog
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
periplasmic space go/ cellular_component
nitric oxide metabolic process go/ biological_process
nitrite reductase (NO-forming) activity go/ molecular_function
beta_rpt_yvtn tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2535
(Mouseover regulator name to see its description)

CAC2535 is regulated by 26 influences and regulates 0 modules.
Regulators for CAC2535 (26)
Regulator Module Operator
CAC0745 45 tf
CAC0865 45 tf
CAC1430 45 tf
CAC1670 45 tf
CAC2616 45 tf
CAC2793 45 tf
CAC2962 45 tf
CAC3214 45 tf
CAC3406 45 tf
CAC3438 45 tf
CAC3509 45 tf
CAC0081 197 tf
CAC0115 197 tf
CAC0549 197 tf
CAC0863 197 tf
CAC1536 197 tf
CAC1670 197 tf
CAC2074 197 tf
CAC2616 197 tf
CAC2859 197 tf
CAC2939 197 tf
CAC2955 197 tf
CAC3406 197 tf
CAC3475 197 tf
CAC3485 197 tf
CAC3579 197 tf

Warning: CAC2535 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
6744 8.70e-05 gGAGG.
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6745 6.60e+03 AgaaGaTAaAgc.A
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7046 5.00e+02 TAagGaGg
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7047 2.10e+03 GTTAcCG
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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 CAC2535

CAC2535 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Uncharacterized conserved protein cog/ cog
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
periplasmic space go/ cellular_component
nitric oxide metabolic process go/ biological_process
nitrite reductase (NO-forming) activity go/ molecular_function
beta_rpt_yvtn tigr/ tigrfam
Module neighborhood information for CAC2535

CAC2535 has total of 24 gene neighbors in modules 45, 197
Gene neighbors (24)
Gene Common Name Description Module membership
CAC0276 CAC0276 Uncharacterized possible metal-binding protein (NCBI ptt file) 45, 135
CAC0562 CAC0562 Predicted membrane protein (NCBI ptt file) 135, 197
CAC0563 CAC0563 Predicted membrane protein (NCBI ptt file) 135, 197
CAC0737 CAC0737 NADP-specific glutamate dehydrogenase (NCBI ptt file) 45, 290
CAC0862 CAC0862 Transmembrane protein (NCBI ptt file) 45, 81
CAC0935 hisZ Histidyl-tRNA synthetase (NCBI ptt file) 15, 197
CAC0936 hisG ATP phosphoribosyltransferase (NCBI ptt file) 15, 197
CAC0937 hisD Histidinol dehydrogenase (NCBI ptt file) 15, 197
CAC0938 hisB Imidazoleglycerol-phosphate dehydratase (NCBI ptt file) 197, 331
CAC0939 hisH Glutamine amidotransferase (NCBI ptt file) 15, 197
CAC0940 hisA Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (NCBI ptt file) 15, 197
CAC0941 hisF Imidazoleglycerol-phosphate synthase (NCBI ptt file) 15, 197
CAC0942 hisI_1 Phosphoribosyl-AMP cyclohydrolase (NCBI ptt file) 15, 197
CAC1236 CAC1236 Hypothetical protein (NCBI ptt file) 45, 135
CAC1487 CAC1487 Uncharacterized protein, similar to TlpA of B.subtilis (NCBI ptt file) 45, 135
CAC1629 CAC1629 Putative intracellular protease/amidase, ThiJ family (NCBI ptt file) 36, 45
CAC2384 CAC2384 Hypothetical protein (NCBI ptt file) 135, 197
CAC2535 CAC2535 Predicted protein of beta-propeller fold (NCBI ptt file) 45, 197
CAC2536 CAC2536 Glycosyltransferase (NCBI ptt file) 45, 81
CAC2537 CAC2537 Predicted phosphatase (NCBI ptt file) 45, 197
CAC3214 CAC3214 Stage V sporulation protein T, AbrB family transcriptional regulator (NCBI ptt file) 45, 135
CAC3318 CAC3318 Hypothetical protein (NCBI ptt file) 45, 203
CAC3540 CAC3540 Hypothetical protein (NCBI ptt file) 45, 135
CAC3547 CAC3547 Uncharacterized conserved membrane protein (NCBI ptt file) 15, 45
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 CAC2535
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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