Organism : Clostridium acetobutylicum | Module List :
CAC1266

Pseudouridylate synthase family protein, yabo B.subtilis ortholog (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1266
(Mouseover regulator name to see its description)

CAC1266 is regulated by 19 influences and regulates 0 modules.
Regulators for CAC1266 (19)
Regulator Module Operator
CAC1264 345 tf
CAC1696 345 tf
CAC1950 345 tf
CAC2055 345 tf
CAC2608 345 tf
CAC2773 345 tf
CAC3424 345 tf
CAC3611 345 tf
CAC0023 67 tf
CAC0299 67 tf
CAC0681 67 tf
CAC0707 67 tf
CAC0841 67 tf
CAC1264 67 tf
CAC1451 67 tf
CAC1588 67 tf
CAC2071 67 tf
CAC2307 67 tf
CAC3149 67 tf

Warning: CAC1266 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
6788 1.70e-02 Aa.aatAagGaGGtg
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6789 4.40e+03 CGCAAGC
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7342 1.60e-09 aAGGgGGA
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7343 7.90e+03 GCTTcGGC
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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 CAC1266

CAC1266 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
Module neighborhood information for CAC1266

CAC1266 has total of 49 gene neighbors in modules 67, 345
Gene neighbors (49)
Gene Common Name Description Module membership
CAC0029 CAC0029 Distantly related to cell wall-associated hydrolases, similar to yycO Bacillus subtilis (NCBI ptt file) 67, 99
CAC0030 CAC0030 Hypothetical protein (NCBI ptt file) 67, 99
CAC0140 CAC0140 Predicted permease (NCBI ptt file) 67, 114
CAC0148 CAC0148 Predicted enzyme with TIM-barrel fold (NCBI ptt file) 117, 345
CAC0160 CAC0160 Predicted acetyltransferase (NCBI ptt file) 185, 345
CAC0177 appB Oligopeptide transport permease protein (NCBI ptt file) 314, 345
CAC0270 CAC0270 Hypothetical protein (NCBI ptt file) 67, 225
CAC0288 CAC0288 ABC transporter, ATP-binding protein (NCBI ptt file) 67, 266
CAC0352 CAC0352 Uncharacterized conserved membrane protein, SANA family (NCBI ptt file) 115, 345
CAC0746 CAC0746 Secreted protease metal-dependent protease (NCBI ptt file) 269, 345
CAC0830 CAC0830 Response regulator (NCBI ptt file) 67, 115
CAC0843 CAC0843 Ribonuclease precursor (barnase), secreted. (NCBI ptt file) 65, 67
CAC0844 CAC0844 Barstar-like protein ribonuclease (barnase) inhibitor (NCBI ptt file) 67, 341
CAC0994 CAC0994 Predicted membrane protein (NCBI ptt file) 100, 345
CAC0995 CAC0995 Predicted membrane protein (NCBI ptt file) 80, 345
CAC1160 CAC1160 Hypothetical protein (NCBI ptt file) 25, 345
CAC1264 lytR Membrane bound transcriptional regulator of LytR family (NCBI ptt file) 67, 248
CAC1266 CAC1266 Pseudouridylate synthase family protein, yabo B.subtilis ortholog (NCBI ptt file) 67, 345
CAC1450 CAC1450 Predicted alpha/beta superfamily hydrolase (NCBI ptt file) 294, 345
CAC1592 CAC1592 Predicted permease, YCGR B.subtilis ortholog (NCBI ptt file) 69, 345
CAC1791 CAC1791 Undecaprenyl pyrophosphate synthase (NCBI ptt file) 282, 345
CAC1911 CAC1911 Hypothetical protein (NCBI ptt file) 117, 345
CAC1950 CAC1950 Hypothetical protein (NCBI ptt file) 117, 345
CAC2040 CAC2040 ABC transported MDR-type, ATPase component (NCBI ptt file) 67, 248
CAC2055 CAC2055 Predicted transcriptional regulator (NCBI ptt file) 158, 345
CAC2122 CAC2122 Conserved membrane protein (NCBI ptt file) 67, 231
CAC2123 sbp Small basic protein, sbp, uncharacterized (NCBI ptt file) 67, 128
CAC2124 CAC2124 Conserved membrane protein (NCBI ptt file) 67, 128
CAC2168 CAC2168 Uncharacterized conserved protein (NCBI ptt file) 258, 345
CAC2287 CAC2287 Acyl-CoA reductase LuxC (NCBI ptt file) 73, 345
CAC2298 CAC2298 Predicted nucleotidyltransferase (NCBI ptt file) 91, 345
CAC2301 mrcB Membrane carboxypeptidase mrcB (NCBI ptt file) 239, 345
CAC2343 CAC2343 LPS biosynthesis O-acetyl transferase (NCBI ptt file) 100, 345
CAC2414 CAC2414 Uncharacterized conserved protein, related to alpha-amylase/alpha-mannosidase (NCBI ptt file) 283, 345
CAC2556 CAC2556 Endoglucanase, family 26; S-layer homology domain (NCBI ptt file) 67, 184
CAC2571 CAC2571 Predicted acetyltransferase (NCBI ptt file) 67, 294
CAC2572 CAC2572 Possible aminoglycoside phosphotransferase (protein kinase related), diverged (NCBI ptt file) 67, 329
CAC2660 pykA Pyruvate carboxylase, PYKA (NCBI ptt file) 29, 345
CAC2687 recQ RecQ protein, superfamily II DNA helicase (NCBI ptt file) 113, 345
CAC2688 CAC2688 Alpha/beta superfamily hydrolase (possible chloroperoxidase) (NCBI ptt file) 67, 238
CAC2694 CAC2694 Hypothetical protein (NCBI ptt file) 158, 345
CAC2752 CAC2752 Uncharacterized membrane protein, YPAA B.subtilis ortholog (NCBI ptt file) 67, 218
CAC2781 CAC2781 Hypothetical protein (NCBI ptt file) 62, 345
CAC2786 CAC2786 Uncharacterized conserved protein, YQGV B.subtilis ortholog (NCBI ptt file) 67, 277
CAC2808 CAC2808 Beta-lactamase class C domain (PBPX family) containing protein (NCBI ptt file) 67, 248
CAC2946 CAC2946 Hypothetical protein (NCBI ptt file) 345, 363
CAC2961 galT Galactose-1-phosphate uridyltransferase (NCBI ptt file) 75, 345
CAC2988 CAC2988 Uncharacterized conserved protein, YABE B.subtilis ortholog (NCBI ptt file) 267, 345
CAC3424 CAC3424 Transcriptional regulator, RpiR family (NCBI ptt file) 158, 345
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 CAC1266
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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