Organism : Clostridium acetobutylicum | Module List :
CAC1226 sigA

RNA polymerase sigma factor (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sigma70-ECF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1226
(Mouseover regulator name to see its description)

CAC1226 is regulated by 18 influences and regulates 17 modules.
Regulators for CAC1226 sigA (18)
Regulator Module Operator
CAC0693 275 tf
CAC1226 275 tf
CAC1426 275 tf
CAC1843 275 tf
CAC1867 275 tf
CAC0113 104 tf
CAC0115 104 tf
CAC0189 104 tf
CAC0254 104 tf
CAC0289 104 tf
CAC0445 104 tf
CAC0627 104 tf
CAC1226 104 tf
CAC1753 104 tf
CAC1941 104 tf
CAC1945 104 tf
CAC2842 104 tf
CAC3579 104 tf

Warning: CAC1226 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
6860 2.80e+00 tttccaCccT.Tc
Loader icon
6861 5.00e+03 gaAGtGaat
Loader icon
7202 3.90e+01 tgGAggTG
Loader icon
7203 1.00e+03 aGAAgt.gagT
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 CAC1226

CAC1226 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sigma70-ECF tigr/ tigrfam
Module neighborhood information for CAC1226

CAC1226 has total of 31 gene neighbors in modules 104, 275
Gene neighbors (31)
Gene Common Name Description Module membership
CAC1112 CAC1112 Hypothetical protein, CF-11 family (NCBI ptt file) 104, 253
CAC1113 CAC1113 Hypothetical protein (NCBI ptt file) 104, 148
CAC1118 CAC1118 Phage related protein (NCBI ptt file) 104, 187
CAC1120 CAC1120 Phage-related protein, YqbO B.subtilis homolog (NCBI ptt file) 104, 220
CAC1164 CAC1164 Hypothetical protein (NCBI ptt file) 101, 104
CAC1165 CAC1165 Hypothetical protein (NCBI ptt file) 4, 104
CAC1174 CAC1174 Hypothetical protein (NCBI ptt file) 104, 253
CAC1175 CAC1175 Hypothetical protein, CF-35 family (NCBI ptt file) 104, 253
CAC1176 CAC1176 Hypothetical protein (NCBI ptt file) 173, 275
CAC1177 CAC1177 Hypothetical protein (NCBI ptt file) 187, 275
CAC1178 CAC1178 Hypothetical protein (NCBI ptt file) 173, 275
CAC1180 CAC1180 Predicted membrane protein (NCBI ptt file) 173, 275
CAC1182 CAC1182 Phage related protein, YorG B.subtilis homolog (NCBI ptt file) 16, 275
CAC1183 CAC1183 Hypothetical protein (NCBI ptt file) 104, 327
CAC1189 CAC1189 Hypothetical protein (NCBI ptt file) 104, 257
CAC1191 CAC1191 Hypothetical protein (NCBI ptt file) 104, 307
CAC1193 CAC1193 Hypothetical protein (NCBI ptt file) 104, 253
CAC1200 CAC1200 Similar to phospho-adenylylsulfate sulfotransferase (NCBI ptt file) 104, 187
CAC1201 CAC1201 Hypothetical protein (NCBI ptt file) 30, 104
CAC1206 CAC1206 Predicted membrane protein (NCBI ptt file) 173, 275
CAC1207 CAC1207 Hypothetical protein (NCBI ptt file) 173, 275
CAC1210 dut Deoxyuridine 5'triphosphate nucleotidohydrolase (DUPTase) (NCBI ptt file) 173, 275
CAC1211 CAC1211 Hypothetical protein (NCBI ptt file) 187, 275
CAC1212 CAC1212 Hypothetical protein (NCBI ptt file) 187, 275
CAC1217 CAC1217 Guanylate kinase (P-loop type) (NCBI ptt file) 104, 275
CAC1218 CAC1218 Phage related protein, YorS B.subtilis homolog (NCBI ptt file) 173, 275
CAC1220 CAC1220 Hypothetical protein (NCBI ptt file) 68, 275
CAC1224 CAC1224 Hypothetical protein (NCBI ptt file) 16, 275
CAC1225 CAC1225 Hypothetical protein (NCBI ptt file) 173, 275
CAC1226 sigA RNA polymerase sigma factor (NCBI ptt file) 104, 275
CAC1227 CAC1227 Hypothetical protein (NCBI ptt file) 104, 181
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 CAC1226
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