Organism : Clostridium acetobutylicum | Module List :
CAC1664 glgP

Glycogen phosphorylase (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Glucan phosphorylase cog/ cog
carbohydrate metabolic process go/ biological_process
glycogen phosphorylase activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
P_ylase tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1664
(Mouseover regulator name to see its description)

CAC1664 is regulated by 25 influences and regulates 0 modules.
Regulators for CAC1664 glgP (25)
Regulator Module Operator
CAC0023 155 tf
CAC0078 155 tf
CAC0289 155 tf
CAC0856 155 tf
CAC1264 155 tf
CAC1467 155 tf
CAC1481 155 tf
CAC1719 155 tf
CAC2084 155 tf
CAC2306 155 tf
CAC3271 155 tf
CAC3409 155 tf
CAC3424 155 tf
CAC0023 18 tf
CAC0078 18 tf
CAC0289 18 tf
CAC1264 18 tf
CAC1467 18 tf
CAC1481 18 tf
CAC1695 18 tf
CAC1869 18 tf
CAC2306 18 tf
CAC3271 18 tf
CAC3409 18 tf
CAC3677 18 tf

Warning: CAC1664 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
6690 7.20e-06 AGGaGG
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6691 1.30e+03 ACcTCcCA
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6962 1.20e+01 tgGAGGT
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6963 4.70e+04 CccCccTTG
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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 CAC1664

CAC1664 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Glucan phosphorylase cog/ cog
carbohydrate metabolic process go/ biological_process
glycogen phosphorylase activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
P_ylase tigr/ tigrfam
Module neighborhood information for CAC1664

CAC1664 has total of 26 gene neighbors in modules 18, 155
Gene neighbors (26)
Gene Common Name Description Module membership
CAC0190 CAC0190 Beta-lactamase (NCBI ptt file) 60, 155
CAC1009 CAC1009 Cell wall biogenesis enzyme (N-terminal domain related to N-Acetylmuramoyl-L-alanine amidase and C-terminal domain related to L-alanoyl-D-glutamate peptidase); peptodoglycan-binding domain (NCBI ptt file) 155, 267
CAC1010 CAC1010 Predicted phosphohydrolase, Icc family (NCBI ptt file) 155, 178
CAC1043 CAC1043 Xre family DNA-binding domain and TPR-repeat containing protein (NCBI ptt file) 18, 184
CAC1072 CAC1072 Fe-S oxidoreductase (NCBI ptt file) 18, 168
CAC1073 CAC1073 Hypothetical protein (NCBI ptt file) 18, 168
CAC1314 CAC1314 Hypothetical protein (NCBI ptt file) 18, 178
CAC1315 CAC1315 Peptodoglycan-binding domain containing protein (NCBI ptt file) 18, 178
CAC1664 glgP Glycogen phosphorylase (NCBI ptt file) 18, 155
CAC1768 CAC1768 Uncharacterized conserved protein, TraB family (NCBI ptt file) 60, 155
CAC1775 CAC1775 Predicted membrane protein (NCBI ptt file) 18, 155
CAC2042 CAC2042 ABC transported MDR-type, permease component (NCBI ptt file) 60, 155
CAC2289 CAC2289 Biotin carboxyl carrier protein (NCBI ptt file) 60, 155
CAC2382 ssb Single-strand DNA-binding protein, ssb (NCBI ptt file) 18, 178
CAC2407 CAC2407 CheY-like receiver domain of response regulator (NCBI ptt file) 7, 155
CAC2408 CAC2408 Glycosyltransferase (NCBI ptt file) 7, 155
CAC2514 CAC2514 Beta galactosidase (NCBI ptt file) 60, 155
CAC2580 CAC2580 Hypothetical protein, CF-41 family (NCBI ptt file) 155, 293
CAC2581 CAC2581 6-pyruvoyl-tetrahydropterin synthase related domain; conserved membrane protein (NCBI ptt file) 18, 178
CAC2663 CAC2663 Protein containing cell-wall hydrolase domain (NCBI ptt file) 130, 155
CAC2678 CAC2678 Hypothetical protein (NCBI ptt file) 18, 184
CAC2944 CAC2944 N-terminal domain intergin-like repeats and c-terminal- cell wall-associated hydrolase domain (NCBI ptt file) 155, 293
CAC3411 CAC3411 Homolog of plant auxin-responsive GH3-like protein (NCBI ptt file) 60, 155
CAC3423 CAC3423 Acetyltransferase (ribosomal protein N-acetylase subfamily) (NCBI ptt file) 18, 178
CAC3558 CAC3558 Probable S-layer protein (NCBI ptt file) 7, 18
CAC3612 CAC3612 Hypothetical protein (NCBI ptt file) 18, 155
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 CAC1664
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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