Organism : Clostridium acetobutylicum | Module List :
CAC0255 nifHD

Nitrogen regulatory protein PII (nitrogen fixation nifHD) (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Nitrogen regulatory protein PII cog/ cog
regulation of nitrogen utilization go/ biological_process
enzyme regulator activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0255
(Mouseover regulator name to see its description)

CAC0255 is regulated by 16 influences and regulates 35 modules.
Regulators for CAC0255 nifHD (16)
Regulator Module Operator
CAC0144 144 tf
CAC0183 144 tf
CAC0255 144 tf
CAC1280 144 tf
CAC2236 144 tf
CAC3433 144 tf
CAC3472 144 tf
CAC3651 144 tf
CAC0254 98 tf
CAC0255 98 tf
CAC0863 98 tf
CAC1668 98 tf
CAC1698 98 tf
CAC1928 98 tf
CAC2236 98 tf
CAC3267 98 tf

Warning: CAC0255 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
6848 3.10e-07 ttggAGGagga
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6849 1.40e+03 AcGtaAaAgccggATgG
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6940 7.40e-04 AGGAgG
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6941 3.00e+03 gaGTA.AgCagtg
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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 CAC0255

CAC0255 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Nitrogen regulatory protein PII cog/ cog
regulation of nitrogen utilization go/ biological_process
enzyme regulator activity go/ molecular_function
Module neighborhood information for CAC0255

CAC0255 has total of 39 gene neighbors in modules 98, 144
Gene neighbors (39)
Gene Common Name Description Module membership
CAC0020 CAC0020 MDR-type permease (NCBI ptt file) 98, 175
CAC0161 CAC0161 ABC transporter (permease) (NCBI ptt file) 108, 144
CAC0206 CAC0206 Uncharacterized conserved membrane protein (NCBI ptt file) 98, 150
CAC0253 nifH Nitrogenase iron protein (nitrogenase component II) gene nifH (NCBI ptt file) 98, 320
CAC0255 nifHD Nitrogen regulatory protein PII (nitrogen fixation nifHD) (NCBI ptt file) 98, 144
CAC0256 nifD Nitrogenase molybdenum-iron protein, alpha chain (nitrogenase component I) gene nifD (NCBI ptt file) 98, 347
CAC0257 nifK Nitrogenase molibdenum-iron protein, beta chain, gene nifK (NCBI ptt file) 144, 169
CAC0341 CAC0341 Predicted membrane protein (NCBI ptt file) 111, 144
CAC0342 CAC0342 Hypothetical protein (NCBI ptt file) 111, 144
CAC0427 CAC0427 Glycerol-3-phosphate ABC-transporter, permease component (NCBI ptt file) 144, 161
CAC0429 CAC0429 Glicerol-3-phosphate ABC-transporter, periplasmic component (NCBI ptt file) 144, 161
CAC0453 CAC0453 ABC-transporter, ATP-binding protein (NCBI ptt file) 111, 144
CAC0544 CAC0544 Permease (NCBI ptt file) 98, 347
CAC0759 CAC0759 Hypothetical protein (NCBI ptt file) 98, 338
CAC0794 CAC0794 Nucleoside-diphosphate-sugar epimerase (UDP-glucose 4-epimerase) (NCBI ptt file) 98, 320
CAC0829 CAC0829 Uncharacterized conserved membrane protein, similar to MDR (VANZ) ORF of Enterococcus (NCBI ptt file) 98, 175
CAC1247 pbpA Penicillin-binding protein 2 (NCBI ptt file) 144, 208
CAC1462 CAC1462 Levanase/invertase (NCBI ptt file) 98, 320
CAC1773 sacC Levanase (NCBI ptt file) 98, 357
CAC2485 CAC2485 Predicted membane protein, probable cation efflux pump (MDR-type) (NCBI ptt file) 144, 161
CAC2532 CAC2532 Protein containing ChW-repeats (NCBI ptt file) 144, 202
CAC2590 CAC2590 Uncharacterized conserved membrane protein (NCBI ptt file) 144, 169
CAC2591 CAC2591 Hypothetical protein, CF-41 family (NCBI ptt file) 144, 169
CAC2674 CAC2674 ATP-dependent superfamily I DNA helicase, PCRA (NCBI ptt file) 3, 98
CAC2707 CAC2707 8-oxoguanine-DNA-glycosylase (NCBI ptt file) 98, 343
CAC2731 CAC2731 Predicted permease (NCBI ptt file) 98, 343
CAC2734 CAC2734 ABC-type multidrug transport system, ATPase component (NCBI ptt file) 71, 98
CAC2736 sbcC ATPase involved in DNA repair (NCBI ptt file) 91, 98
CAC2804 CAC2804 Predicted Zn-dependent hydrolase from metallo-beta-lactamase superfamily (NCBI ptt file) 144, 169
CAC2862 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI ptt file) 78, 98
CAC3269 CAC3269 ABC-type MDR transport system, ATPase component (NCBI ptt file) 144, 230
CAC3300 gerKA Spore germination protein GerKA, membrane protein (NCBI ptt file) 144, 338
CAC3304 CAC3304 Hypothetical protein, CF-42 family (NCBI ptt file) 22, 98
CAC3439 CAC3439 Uncharacterized conserved membrane protein, YGAE B.subtilis homolog (NCBI ptt file) 144, 320
CAC3447 CAC3447 Protein-disulfide isomerases DsbC/DsbG (NCBI ptt file) 144, 338
CAC3498 CAC3498 Sugar kinase, ribokinase family (NCBI ptt file) 98, 175
CAC3499 CAC3499 Predicted endonuclease (NCBI ptt file) 98, 338
CAC3582 CAC3582 Hypothetical protein (NCBI ptt file) 98, 103
CAC3585 CAC3585 ABC-type transporter, ATPase component (NCBI ptt file) 98, 103
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 CAC0255
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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