Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2214

Nitrogen-fixing NifU (NCBI)

CircVis
Functional Annotations (4)
Function System
Thioredoxin-like proteins and domains cog/ cog
iron ion binding go/ molecular_function
iron-sulfur cluster assembly go/ biological_process
iron-sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2214
(Mouseover regulator name to see its description)

RSP_2214 is regulated by 26 influences and regulates 0 modules.
Regulators for RSP_2214 (26)
Regulator Module Operator
RSP_0958 46 tf
RSP_0999 46 tf
RSP_1092 46 tf
RSP_1139 46 tf
RSP_1669 46 tf
RSP_1890 46 tf
RSP_2130 46 tf
RSP_2200 46 tf
RSP_2236 46 tf
RSP_2410 46 tf
RSP_2610 46 tf
RSP_3094 46 tf
RSP_3324 46 tf
RSP_0122 35 tf
RSP_0794 35 tf
RSP_0958 35 tf
RSP_0999 35 tf
RSP_1139 35 tf
RSP_1550 35 tf
RSP_1871 35 tf
RSP_2410 35 tf
RSP_2681 35 tf
RSP_2801 35 tf
RSP_3226 35 tf
RSP_3324 35 tf
RSP_3621 35 tf

Warning: RSP_2214 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
7790 1.70e+03 atatCaTtgaaAAat
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7791 2.80e+04 TTATAT
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7812 3.10e+02 GAaAGga
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7813 1.30e+03 TCAcAaa.aGa.AAT
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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 RSP_2214

RSP_2214 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Thioredoxin-like proteins and domains cog/ cog
iron ion binding go/ molecular_function
iron-sulfur cluster assembly go/ biological_process
iron-sulfur cluster binding go/ molecular_function
Module neighborhood information for RSP_2214

RSP_2214 has total of 45 gene neighbors in modules 35, 46
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_0244 RSP_0244 Predicted glutamine amidotransferases (NCBI) 46, 161
RSP_0458 RSP_0458 hypothetical protein (NCBI) 35, 64
RSP_0583 RSP_0583 hypothetical protein (NCBI) 35, 287
RSP_0612 RSP_0612 RhtB family transporter (NCBI) 35, 171
RSP_0715 RSP_0715 Ribonuclease T2 (NCBI) 10, 35
RSP_0754 RSP_0754 hypothetical protein (NCBI) 35, 250
RSP_0822 RSP_0822 hypothetical protein (NCBI) 35, 341
RSP_1056 RSP_1056 periplasmic sensor signal transduction histidine kinase (NCBI) 46, 195
RSP_1104 RSP_1104 hypothetical protein (NCBI) 35, 327
RSP_1106 rbfA Ribosome-binding factor A (NCBI) 46, 149
RSP_1141 RSP_1141 hypothetical protein (NCBI) 35, 250
RSP_1174 pip Prolyl aminopeptidase (NCBI) 35, 323
RSP_1497 RSP_1497 Putative outer membrane lipoprotein carrier protein (NCBI) 46, 287
RSP_1551 RSP_1551 putative glyoxalase family protein (NCBI) 35, 250
RSP_1611 RSP_1611 sensor histidine kinase (NCBI) 35, 370
RSP_1678 RSP_1678 putative RecO protein (NCBI) 35, 341
RSP_1823 mog Molybdenum cofactor biosynthesis protein (NCBI) 35, 162
RSP_1824 adh Zinc-containing alcohol dehydrogenase (NCBI) 35, 97
RSP_1844 RSP_1844 hypothetical protein (NCBI) 35, 329
RSP_1852 RSP_1852 hypothetical protein (NCBI) 46, 161
RSP_1873 RSP_1873 hypothetical protein (NCBI) 35, 216
RSP_1890 RSP_1890 Transcriptional regulator, LysR family (NCBI) 46, 52
RSP_2115 envA putative UDP-3-O-acyl N-acetylglucosamine deacetylase (NCBI) 46, 287
RSP_2136 RSP_2136 hypothetical protein (NCBI) 35, 262
RSP_2214 RSP_2214 Nitrogen-fixing NifU (NCBI) 35, 46
RSP_2218 RSP_2218 hypothetical protein (NCBI) 46, 287
RSP_2264 telA Tellurite resistance protein (NCBI) 46, 366
RSP_2286 RSP_2286 hypothetical protein (NCBI) 23, 35
RSP_2421 RSP_2421 hypothetical protein (NCBI) 35, 162
RSP_2481 cysE serine acetyltransferase (NCBI) 46, 64
RSP_2554 RSP_2554 hypothetical protein (NCBI) 35, 250
RSP_2625 nifU NifU-related protein involved in Fe-S cluster formation (NCBI) 46, 48
RSP_2631 RSP_2631 USG protein (NCBI) 35, 250
RSP_2639 RSP_2639 Putative arginine-tRNA protein transferase (NCBI) 46, 200
RSP_2671 RSP_2671 hypothetical protein (NCBI) 35, 185
RSP_2776 acpP Acyl carrier protein, AcpP (NCBI) 46, 48
RSP_2937 RSP_2937 hypothetical protein (NCBI) 35, 341
RSP_3228 RSP_3228 Predicted mannose-6-phosphate isomerase (NCBI) 35, 185
RSP_3307 RSP_3307 hypothetical protein (NCBI) 35, 185
RSP_3324 RSP_3324 transcriptional regulator, LuxR family (NCBI) 46, 286
RSP_3378 RSP_3378 hypothetical protein (NCBI) 35, 46
RSP_3594 RSP_3594 Antifreeze protein, type I (NCBI) 35, 185
RSP_3646 RSP_3646 DNA topology modulation kinase FlaR, putative (NCBI) 46, 63
RSP_3810 RSP_3810 hypothetical protein (NCBI) 35, 112
RSP_4314 RSP_4314 tRNA-Ser (NCBI) 35, 48
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 RSP_2214
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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