Organism : Clostridium acetobutylicum | Module List :
CAC1509

Specialized sigma subunit of RNA polymerase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog 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 CAC1509
(Mouseover regulator name to see its description)

CAC1509 is regulated by 26 influences and regulates 10 modules.
Regulators for CAC1509 (26)
Regulator Module Operator
CAC0360 305 tf
CAC0821 305 tf
CAC1426 305 tf
CAC1467 305 tf
CAC1509 305 tf
CAC1578 305 tf
CAC2209 305 tf
CAC2254 305 tf
CAC2259 305 tf
CAC2306 305 tf
CAC2955 305 tf
CAC3496 305 tf
CAC3509 305 tf
CAC3695 305 tf
CAC0681 367 tf
CAC0841 367 tf
CAC1509 367 tf
CAC1670 367 tf
CAC1695 367 tf
CAC2476 367 tf
CAC2568 367 tf
CAC2616 367 tf
CAC2859 367 tf
CAC3438 367 tf
CAC3651 367 tf
CAC3673 367 tf

Warning: CAC1509 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
7262 4.30e+00 AGg.GG
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7263 2.30e+02 CcCCCC
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7382 7.10e+03 Ag.aGGcTA
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7383 3.30e+03 CaCCTC
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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 CAC1509

CAC1509 is enriched for 6 functions in 3 categories.
Module neighborhood information for CAC1509

CAC1509 has total of 33 gene neighbors in modules 305, 367
Gene neighbors (33)
Gene Common Name Description Module membership
CAC0014 CAC0014 Aminotransferase (NCBI ptt file) 250, 305
CAC0092 CAC0092 Uncharacterized predicted membrane protein, YTWI B.subtilis ortholog (NCBI ptt file) 305, 363
CAC0486 CAC0486 Hypothetical protein (NCBI ptt file) 73, 367
CAC0642 CAC0642 Conserved domain seen in the bacterial SpoT (NCBI ptt file) 73, 367
CAC0668 CAC0668 Predicted membrane protein (NCBI ptt file) 174, 305
CAC0681 nrgB Nitrogen regulatory protein PII, gene nrgB (NCBI ptt file) 235, 367
CAC0803 CAC0803 Hypothetical protein (NCBI ptt file) 328, 367
CAC0824 CAC0824 Thioredoxin (NCBI ptt file) 305, 334
CAC0841 CAC0841 Predicted transcriptional regulator (NCBI ptt file) 15, 367
CAC1020 CAC1020 Hypothetical protein (NCBI ptt file) 80, 367
CAC1055 CAC1055 Hypothetical protein (NCBI ptt file) 38, 367
CAC1253 CAC1253 Sporulation protein IVFB related protein, predicted metallopeptidase (NCBI ptt file) 95, 367
CAC1486 CAC1486 Uncharacterized protein, ortholog of YKUS B.subtilis (NCBI ptt file) 118, 367
CAC1509 CAC1509 Specialized sigma subunit of RNA polymerase (NCBI ptt file) 305, 367
CAC1510 CAC1510 Hypothetical protein (NCBI ptt file) 293, 305
CAC1567 CAC1567 Hypothetical protein (NCBI ptt file) 95, 367
CAC1609 CAC1609 Zn-finger containing protein (NCBI ptt file) 293, 305
CAC2465 CAC2465 Uncharacterized conserved protein (NCBI ptt file) 73, 367
CAC2488 CAC2488 Uncharacterized conserved protein, YTFE family (NCBI ptt file) 285, 367
CAC2517 nrpE Extracellular neutral metalloprotease, NPRE (NCBI ptt file) 269, 305
CAC2802 CAC2802 Predicted phosphoglycerol transferase (alkaline phosphatase superfamily), YFNI B.subtilis (NCBI ptt file) 73, 367
CAC2876 CAC2876 Deoxycytidylate deaminase (NCBI ptt file) 15, 367
CAC3019 CAC3019 Sensory transduction protein with GGDEF and EAL domains (NCBI ptt file) 73, 367
CAC3169 ilvB Acetolactate synthase large subunit (NCBI ptt file) 305, 334
CAC3170 ilvD Dihydroxy-acid dehydratase (NCBI ptt file) 305, 334
CAC3171 leuB Isopropylmalate dehydrogenase (NCBI ptt file) 305, 334
CAC3172 leuD 3-isopropylmalate dehydratase, small subunit (NCBI ptt file) 305, 334
CAC3173 leuC 3-Isopropylmalate dehydratase, large subunit (NCBI ptt file) 305, 334
CAC3174 leuA 2-isopropylmalate synthase (NCBI ptt file) 305, 334
CAC3176 ilvN Acetolactate synthase, small subunit (NCBI ptt file) 29, 367
CAC3205 spoIIE Stage II sporulation protein E, serine phosphatase family (NCBI ptt file) 42, 367
CAC3393 CAC3393 Hypothetical protein (NCBI ptt file) 80, 367
CAC3727 CAC3727 Uncharacterized protein, YYAC B.subtilis homolog (NCBI ptt file) 95, 367
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 CAC1509
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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