Organism : Methanococcus maripaludis S2 | Module List :
MMP1361 rpoB2

DNA-directed RNA polymerase subunit beta''

CircVis
Functional Annotations (10)
Function System
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1361
(Mouseover regulator name to see its description)

MMP1361 is regulated by 19 influences and regulates 0 modules.
Regulators for MMP1361 rpoB2 (19)
Regulator Module Operator
MMP0033 25 tf
MMP0052
MMP0257
25 combiner
MMP0052
MMP0480
25 combiner
MMP0907
MMP1646
25 combiner
MMP1704 25 tf
MMP0033 149 tf
MMP0052
MMP0480
149 combiner
MMP0607 149 tf
MMP0637
MMP0678
149 combiner
MMP1467
MMP1646
149 combiner
MMP1704 149 tf
MMP0052 92 tf
MMP0052
MMP0257
92 combiner
MMP0257 92 tf
MMP0257
MMP1376
92 combiner
MMP0568
MMP1100
92 combiner
MMP0907 92 tf
MMP0052
MMP0257
109 combiner
MMP0907
MMP1646
109 combiner

Warning: MMP1361 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 8 motifs predicted.

Motif Table (8)
Motif Id e-value Consensus Motif Logo
711 5.90e+00 caagGAg.actcGcTgcAac
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712 9.90e+02 TtAaTCTGGtG
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841 3.90e+02 ccGGtGat
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842 3.30e+03 GGCGCcAtCC
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875 2.20e+02 GGaGgc
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876 8.70e+03 GCGAGAaG
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947 6.00e-01 taTTaa.cggtGgt
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948 1.50e+02 tCTgtcc.tct.gga.gcat
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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 MMP1361

MMP1361 is enriched for 10 functions in 4 categories.
Enrichment Table (10)
Function System
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
Module neighborhood information for MMP1361

MMP1361 has total of 83 gene neighbors in modules 25, 92, 109, 149
Gene neighbors (83)
Gene Common Name Description Module membership
MMP0026 DP2 DNA polymerase II large subunit 25, 41, 92
MMP0033 LysR family protein 87, 109
MMP0034 GTP cyclohydrolase 130, 149
MMP0036 tfe transcription initiation factor E subunit alpha 49, 87, 92, 129
MMP0043 isopentenyl pyrophosphate isomerase 61, 92
MMP0092 rpoF DNA-directed RNA polymerase subunit F 87, 109
MMP0099 major facilitator transporter 14, 92
MMP0133 guaB inosine-5'-monophosphate dehydrogenase 25, 120, 140
MMP0134 hypothetical protein MMP0134 24, 92
MMP0137 dys putative deoxyhypusine synthase 25, 141, 149
MMP0243 hypothetical protein MMP0243 4, 25, 38
MMP0246 hypothetical protein MMP0246 87, 109
MMP0247 ribosomal biogenesis protein 87, 109
MMP0248 DNA-directed RNA polymerase-like protein 87, 109
MMP0284 infB translation initiation factor IF-2 25, 149
MMP0315 iorB1 indolepyruvate oxidoreductase subunit B 25, 64
MMP0316 iorA1 indolepyruvate oxidoreductase subunit alpha 1 25, 64, 87
MMP0319 cbiL precorrin-2 C-20 methyltransferase 24, 140, 141, 149
MMP0340 pycB pyruvate carboxylase subunit B 24, 86, 120, 141, 149
MMP0405 gch3 GTP cyclohydrolase III 19, 92
MMP0412 MiaB-like tRNA modifying protein 4, 25, 87
MMP0415 O-sialoglycoprotein endopeptidase/protein kinase 47, 149
MMP0457 DEAD/DEAH box helicase domain-containing protein 61, 92
MMP0530 hypothetical protein MMP0530 92, 140
MMP0564 hypothetical protein MMP0564 111, 149
MMP0566 AMP-binding domain-containing protein 92, 109
MMP0568 transcriptional regulator-like protein 109, 162
MMP0588 dph5 diphthine synthase 25, 81, 140
MMP0603 aIF-1A translation initiation factor IF-1A 29, 87, 109, 162
MMP0604 hypothetical protein MMP0604 87, 109
MMP0610 tgtA 7-cyano-7-deazaguanine tRNA-ribosyltransferase 25, 41
MMP0639 50S ribosomal protein L24e 16, 92, 130
MMP0640 rps28e 30S ribosomal protein S28e 16, 92, 130
MMP0641 rpl7ae 50S ribosomal protein L7Ae 16, 92, 130
MMP0682 hypothetical protein MMP0682 67, 92
MMP0694 beta-lactamase-like protein 51, 109, 149
MMP0695 psmB proteasome subunit beta 51, 92
MMP0707 sodium/hydrogen exchanger 87, 109, 140
MMP0760 hypothetical protein MMP0760 22, 67, 92
MMP0878 ribonuclease P-like protein 25, 87, 140
MMP0905 hypothetical protein MMP0905 14, 149
MMP0906 ribonuclease Z 129, 149
MMP0907 transcriptional regulator TrmB 14, 149
MMP0921 RNAse P, Rpr2/Rpp21 subunit 25, 141
MMP0941 hypothetical protein MMP0941 129, 149
MMP0943 taqD glycerol-3-phosphate cytidyltransferase 92, 111
MMP0953 cbiH precorrin-3B C17-methyltransferase 24, 25, 149
MMP0975 modA molybdenum ABC transporter solute-binding protein 64, 92
MMP1011 gltX glutamyl-tRNA synthetase 25, 129
MMP1014 radical SAM domain-containing protein 25, 141
MMP1048 hypothetical protein MMP1048 14, 25
MMP1085 hypothetical protein MMP1085 141, 143, 149
MMP1108 corA magnesium/cobalt transporter CorA 141, 149
MMP1112 hypothetical protein MMP1112 111, 129, 141, 149
MMP1114 rpe Pentose-5-phosphate 3-epimerase 109, 120
MMP1115 transketolase, N terminal half 109, 120
MMP1195 yneG putative cytoplasmic protein 25, 126
MMP1211 hypothetical protein MMP1211 89, 92
MMP1289 rpl10e 50S ribosomal protein L10e 3, 92, 105
MMP1307 methyltransferase-like protein 4, 149
MMP1319 rps13p 30S ribosomal protein S13P 92, 103, 118
MMP1327 rpoK RNA polymerase Rpb6 103, 139, 149
MMP1328 enolase 103, 139, 149
MMP1356 PP-loop domain-containing protein 25, 129, 139, 140, 149
MMP1357 hypothetical protein MMP1357 140, 149
MMP1361 rpoB2 DNA-directed RNA polymerase subunit beta'' 25, 92, 109, 149
MMP1379 thyA thymidylate synthase 64, 92
MMP1380 chlorohydrolase 51, 92
MMP1381 beta-lactamase-like protein 51, 92
MMP1396 aminotransferase 64, 92
MMP1400 hypothetical protein MMP1400 61, 92, 97, 105
MMP1403 rpl22p 50S ribosomal protein L22P 3, 61, 92, 96, 97, 105
MMP1425 tRNA 2'-O-methylase 25, 87, 140
MMP1443 ATP/GTP-binding motif-containing protein 20, 61, 92
MMP1444 methionine aminopeptidase 20, 51, 61, 92
MMP1480 aconitase family 60, 87, 92
MMP1491 trzA amidohydrolase 14, 111, 122, 149
MMP1492 pyrE orotate phosphoribosyltransferase 14, 149
MMP1511 amino acid carrier protein 19, 92
MMP1543 rpl3p 50S ribosomal protein L3P 63, 92, 128
MMP1582 pdaD pyruvoyl-dependent arginine decarboxylase 87, 149
MMP1614 hisS histidyl-tRNA synthetase 141, 149
MMP1710 hypothetical protein MMP1710 20, 87, 92
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 MMP1361
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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