Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3600 miaB

MiaB tRNA modification protein (Radical SAM) (NCBI)

CircVis
Functional Annotations (5)
Function System
2-methylthioadenine synthetase cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
TIGR00089 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3600
(Mouseover regulator name to see its description)

RSP_3600 is regulated by 31 influences and regulates 0 modules.
Regulators for RSP_3600 miaB (31)
Regulator Module Operator
RSP_0386 311 tf
RSP_0443 311 tf
RSP_0623 311 tf
RSP_1163 311 tf
RSP_1231 311 tf
RSP_1712 311 tf
RSP_1739 311 tf
RSP_1741 311 tf
RSP_2494 311 tf
RSP_2533 311 tf
RSP_2801 311 tf
RSP_2850 311 tf
RSP_3238 311 tf
RSP_3433 311 tf
RSP_3664 311 tf
RSP_3665 311 tf
RSP_0386 271 tf
RSP_0443 271 tf
RSP_0547 271 tf
RSP_0623 271 tf
RSP_0999 271 tf
RSP_1092 271 tf
RSP_1225 271 tf
RSP_1231 271 tf
RSP_1739 271 tf
RSP_1776 271 tf
RSP_2027 271 tf
RSP_2130 271 tf
RSP_2494 271 tf
RSP_3238 271 tf
RSP_3317 271 tf

Warning: RSP_3600 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
8258 9.70e-04 CacAAgCCgaaGgat.TgC
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8259 4.50e+00 GGGaaGaAGCGGacAaAcGT
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8336 8.50e-01 CcTTCGCGCCCCGgTtTCacaGga
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8337 3.90e+01 AcTcAAC.GaA.CGGccttCCtgt
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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_3600

RSP_3600 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
2-methylthioadenine synthetase cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
TIGR00089 tigr/ tigrfam
Module neighborhood information for RSP_3600

RSP_3600 has total of 46 gene neighbors in modules 271, 311
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0164 RSP_0164 hypothetical protein (NCBI) 75, 311
RSP_0248 RSP_0248 elongation factor EF-P (NCBI) 203, 311
RSP_0425 metG Methionyl-tRNA synthetase (NCBI) 311, 316
RSP_0448 RSP_0448 EF-Tu; elongation factor Tu (NCBI) 209, 271
RSP_0490 RSP_0490 carbohydrate kinase (NCBI) 271, 363
RSP_0705 RSP_0705 Cytochrome cy (NCBI) 58, 271
RSP_0706 pheA Prephenate dehydratase (NCBI) 263, 271
RSP_0901 RSP_0901 N-6 Adenine-specific DNA methylase (NCBI) 142, 271
RSP_0902 RSP_0902 Hydrolase, haloacid dehalogenase-like hydrolase (NCBI) 142, 271
RSP_1050 RSP_1050 Acetyltransferase (GNAT) family (NCBI) 5, 271
RSP_1051 RSP_1051 hypothetical protein (NCBI) 5, 271
RSP_1052 RSP_1052 possible Acetyltransferase (NCBI) 268, 271
RSP_1110 RSP_1110 hypothetical protein (NCBI) 209, 271
RSP_1132 RSP_1132 hypothetical protein (NCBI) 263, 271
RSP_1146 gltB Glutamine-pyruvate aminotransferase (NCBI) 231, 271
RSP_1197 HemH Ferrochelatase (NCBI) 209, 311
RSP_1404 RSP_1404 Orotidine 5'-phosphate decarboxylase (NCBI) 311, 381
RSP_1474 nspC putative carboxynorspermidine decarboxylase protein (NCBI) 271, 323
RSP_1475 RSP_1475 saccharopine dehydrogenase family (NCBI) 271, 311
RSP_1575 sopT sulfate adenylyltransferase (NCBI) 109, 271
RSP_1849 RSP_1849 Aspartate kinase (NCBI) 109, 271
RSP_1926 RSP_1926 tRNA-Dihydrouridine synthase (NCBI) 214, 311
RSP_1929 pyrE Orotate phosphoribosyltransferase (NCBI) 124, 311
RSP_2144 cfaS Cyclopropane-fatty-acyl-phospholipid synthase CfaS (NCBI) 299, 311
RSP_2284 RSP_2284 Histidinol-phosphate aminotransferase (NCBI) 311, 356
RSP_2303 RSP_2303 hypothetical protein (NCBI) 54, 271
RSP_2696 RSP_2696 ABC transporter, fused ATPase and inner membrane subunits (NCBI) 214, 311
RSP_2699 RSP_2699 Probable GTP-binding protein (NCBI) 166, 271
RSP_2717 RSP_2717 putative UUP ATPase (NCBI) 214, 311
RSP_2739 RSP_2739 hypothetical protein (NCBI) 5, 271
RSP_2977 prfB Peptide chain release factor 2 (NCBI) 271, 311
RSP_2980 aspAT Putative aspartate aminotransferase A (NCBI) 281, 311
RSP_2981 RSP_2981 Putative protein-disulfide isomerase (NCBI) 277, 311
RSP_3045 dorR DMSO/TMAO-two component transcriptional regulator, winged helix family (NCBI) 218, 311
RSP_3547 RSP_3547 Ribonucleotide reductase (NCBI) 271, 311
RSP_3548 RSP_3548 hypothetical protein (NCBI) 181, 271
RSP_3591 RSP_3591 cytidylate kinase (NCBI) 209, 271
RSP_3600 miaB MiaB tRNA modification protein (Radical SAM) (NCBI) 271, 311
RSP_3710 RSP_3710 Monovalent cation/proton antiporter subunit/mnhG (NCBI) 311, 361
RSP_3711 RSP_3711 Multisubunit Na+/H+ antiporter MnhF subunit (NCBI) 311, 361
RSP_3712 RSP_3712 Multisubunit Na+/H+ antiporter MnhE subunit (NCBI) 311, 383
RSP_3713 RSP_3713 pH adaptation potassium efflux system, phaD subunit (NCBI) 311, 383
RSP_3714 RSP_3714 pH adaption potassium efflux system, phaC subunit (NCBI) 311, 361
RSP_3715 RSP_3715 pH adaption potassium efflux system, PhaB subunit (NCBI) 311, 361
RSP_3716 selD selenide, water dikinase (selenophosphate synthetase) (NCBI) 279, 311
RSP_3829 RSP_3829 tRNA/rRNA methyltransferase (SpoU) (NCBI) 263, 271
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_3600
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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