Organism : Clostridium acetobutylicum | Module List :
CAC0929

SAM-dependent methyltransferase (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
SAM-dependent methyltransferases cog/ cog
metabolic process go/ biological_process
methyltransferase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0929
(Mouseover regulator name to see its description)

CAC0929 is regulated by 20 influences and regulates 10 modules.
Regulators for CAC0929 (20)
Regulator Module Operator
CAC0231 37 tf
CAC0856 37 tf
CAC0929 37 tf
CAC0933 37 tf
CAC1032 37 tf
CAC1559 37 tf
CAC1945 37 tf
CAC1947 37 tf
CAC2236 37 tf
CAC3166 37 tf
CAC0093 23 tf
CAC0189 23 tf
CAC0231 23 tf
CAC0856 23 tf
CAC0929 23 tf
CAC1032 23 tf
CAC2222 23 tf
CAC2236 23 tf
CAC3345 23 tf
CAC3418 23 tf

Warning: CAC0929 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
6700 4.20e-01 GGggG.AG
Loader icon
6701 3.00e+01 gggaA.TaAA.Ttct.ccT
Loader icon
6728 1.40e-05 GaTAAttAGaGtgGtAccGcg
Loader icon
6729 2.60e+01 GgagGtc
Loader icon
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 CAC0929

CAC0929 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
SAM-dependent methyltransferases cog/ cog
metabolic process go/ biological_process
methyltransferase activity go/ molecular_function
Module neighborhood information for CAC0929

CAC0929 has total of 22 gene neighbors in modules 23, 37
Gene neighbors (22)
Gene Common Name Description Module membership
CAC0102 CAC0102 O-acetylhomoserine sulfhydrylase (NCBI ptt file) 23, 37
CAC0103 cysC Adenylylsulfate kinase (NCBI ptt file) 23, 37
CAC0104 CAC0104 Adenylylsulfate reductase, subunit A (NCBI ptt file) 23, 37
CAC0105 CAC0105 Ferredoxin (NCBI ptt file) 23, 37
CAC0106 CAC0106 ABC-type probable sulfate transporter, periplasmic binding protein (NCBI ptt file) 23, 37
CAC0107 CAC0107 ABC-type sulfate transporter, ATPase component (NCBI ptt file) 23, 37
CAC0108 CAC0108 ABC-type probable sulfate transporter, permease protein (NCBI ptt file) 23, 37
CAC0109 cysD Sulfate adenylate transferase, CysD subfamily (NCBI ptt file) 23, 37
CAC0110 cysN GTPase, sulfate adenylate transferase subunit 1 (NCBI ptt file) 23, 37
CAC0880 CAC0880 Periplasmic amino acid binding protein (NCBI ptt file) 23, 147
CAC0929 CAC0929 SAM-dependent methyltransferase (NCBI ptt file) 23, 37
CAC0930 metB Cystathionine gamma-synthase (NCBI ptt file) 23, 37
CAC0931 CAC0931 Cysteine synthase (NCBI ptt file) 23, 37
CAC0932 CAC0932 Hypothetical protein (NCBI ptt file) 23, 321
CAC2235 cysK Cysteine synthase/cystathionine beta-synthase, CysK (NCBI ptt file) 23, 27
CAC2976 CAC2976 Glu-tRNAGln amidotransferase subunit B (NCBI ptt file) 37, 221
CAC2979 aspS Aspartyl-tRNA synthetase (NCBI ptt file) 37, 238
CAC3325 CAC3325 Periplasmic amino acid binding protein (NCBI ptt file) 23, 37
CAC3326 CAC3326 Amino acid ABC-type transporter, permease component (NCBI ptt file) 23, 37
CAC3327 CAC3327 Amino acid ABC-type transporter, ATPase component (NCBI ptt file) 23, 37
CAC3664 CAC3664 Predicted flavodoxin (NCBI ptt file) 23, 147
CAC3665 CAC3665 Alpha/beta superfamily hydrolase (NCBI ptt file) 23, 167
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 CAC0929
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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