Organism : Methanococcus maripaludis S2 | Module List :
MMP1303

sensory transduction histidine kinase

CircVis
Functional Annotations (6)
Function System
Signal transduction histidine kinase cog/ cog
two-component sensor activity go/ molecular_function
ATP binding go/ molecular_function
signal transduction go/ biological_process
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1303
(Mouseover regulator name to see its description)

MMP1303 is regulated by 6 influences and regulates 12 modules.
Regulators for MMP1303 (6)
Regulator Module Operator
MMP1467 66 tf
MMP0031
MMP1646
28 combiner
MMP1052 28 tf
MMP1052
MMP1137
28 combiner
MMP1100
MMP1442
28 combiner
MMP1100
MMP1646
28 combiner

Warning: MMP1303 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
669 2.30e-02 GtGtgCtcccaac
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670 1.10e+04 GGGggAACc
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717 2.80e-04 Aaat.GGtGa
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718 2.30e+01 cgGgaGTTcG
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793 4.50e+02 TttCTtt..tA.aATccccG
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794 1.70e+03 GaTGCAGT
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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 MMP1303

MMP1303 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Signal transduction histidine kinase cog/ cog
two-component sensor activity go/ molecular_function
ATP binding go/ molecular_function
signal transduction go/ biological_process
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
Module neighborhood information for MMP1303

MMP1303 has total of 94 gene neighbors in modules 4, 28, 66
Gene neighbors (94)
Gene Common Name Description Module membership
Antisense_8 None 28, 153
MMP0011 DNA-cytosine methyltransferase 4, 104
MMP0014 truD tRNA pseudouridine synthase D 66, 107
MMP0015 hypothetical protein MMP0015 66, 107
MMP0022 hypothetical protein MMP0022 13, 66
MMP0023 hypothetical protein MMP0023 13, 66
MMP0072 hypothetical protein MMP0072 28, 129
MMP0105 hypothetical protein MMP0105 4, 107
MMP0140 (NiFe) hydrogenase maturation protein HypF 4, 85
MMP0165 ABC transporter 28, 115
MMP0166 MATE family drug/sodium antiporter 1, 28
MMP0167 ABC transporter ATP-binding protein 1, 28
MMP0168 ParR family transcriptional regulator 1, 28
MMP0179 purL phosphoribosylformylglycinamidine synthase 66, 143
MMP0181 hypothetical protein MMP0181 4, 58
MMP0216 cation transport ATPase 4, 41, 95
MMP0243 hypothetical protein MMP0243 4, 25, 38
MMP0256 hisH imidazole glycerol phosphate synthase subunit HisH 28, 58
MMP0257 tbp transcription factor 28, 58
MMP0265 hypothetical protein MMP0265 28, 129
MMP0296 hypothetical protein MMP0296 4, 129
MMP0313 hypothetical protein MMP0313 28, 73
MMP0333 hypothetical protein MMP0333 4, 126
MMP0342 hypothetical protein MMP0342 28, 98
MMP0392 purD phosphoribosylamine--glycine ligase 4, 75, 104
MMP0401 metE methionine synthase 4, 15, 80
MMP0412 MiaB-like tRNA modifying protein 4, 25, 87
MMP0447 nitrogenase-like protein 4, 146
MMP0448 hypothetical protein MMP0448 4, 70
MMP0479 hypothetical protein MMP0479 4, 95
MMP0499 hypothetical protein MMP0499 22, 28, 144, 146, 153
MMP0503 hypothetical protein MMP0503 4, 126
MMP0511 fmdB molybdenum containing formylmethanofuran dehydrogenase subunit B 5, 28
MMP0524 hypothetical protein MMP0524 4, 58, 146, 153, 163
MMP0525 hypothetical protein MMP0525 4, 146, 163
MMP0536 hypothetical protein MMP0536 1, 28
MMP0571 moaA molybdenum cofactor biosynthesis protein A 4, 89
MMP0608 2-hydroxyglutaryl-CoA dehydratase subunit A-like protein 1, 28
MMP0609 pth2 peptidyl-tRNA hydrolase 66, 140
MMP0630 feoB ferrous iron transporter 28, 76, 106, 121
MMP0631 putative iron dependent repressor 28, 121, 144
MMP0684 hsp20 heat shock protein Hsp20 28, 121
MMP0812 hypothetical protein MMP0812 12, 28
MMP0843 hypothetical protein MMP0843 22, 28
MMP0844 hypothetical protein MMP0844 66, 133
MMP0868 proV ABC transporter ATPase 41, 66
MMP0886 cobalt ABC transporter inner membrane protein 4, 151
MMP0936 aroE shikimate 5-dehydrogenase 66, 107
MMP0945 glyceraldehyde-3-phosphate ferredoxin oxidoreductase 66, 98
MMP0948 hypothetical protein MMP0948 4, 115
MMP0949 tRNA CCA-pyrophosphorylase 4, 70
MMP1000 hypothetical protein MMP1000 4, 95
MMP1034 tmk thymidylate kinase 66, 68
MMP1051 surE stationary phase survival protein SurE 12, 28, 106
MMP1064 adenylate cyclase 4, 51
MMP1066 putative molybdenum cofactor biosynthesis protein MoaC 28, 133
MMP1082 hisH imidazole glycerol phosphate synthase subunit HisH 66, 143
MMP1090 NAD-dependent epimerase/dehydratase 66, 133
MMP1095 phosphate-binding protein 66, 89
MMP1096 phosphate ABC transporter inner membrane protein 66, 89
MMP1097 phosphate ABC transporter inner membrane protein 66, 89
MMP1098 pstB phosphate ABC transporter ATP-binding protein 66, 89
MMP1099 phosphate transporter PhoU 66, 89, 95
MMP1130 hypothetical protein MMP1130 4, 38
MMP1150 mtaA uroporphyrinogen decarboxylase 4, 41, 95
MMP1171 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase 28, 66
MMP1228 hypothetical protein MMP1228 4, 22, 142
MMP1265 glutamyl-tRNA(Gln) amidotransferase subunit E 28, 129
MMP1303 sensory transduction histidine kinase 4, 28, 66
MMP1304 response regulator receiver protein 4, 126
MMP1305 hypothetical protein MMP1305 4, 126
MMP1307 methyltransferase-like protein 4, 149
MMP1454 ehaG hypothetical protein MMP1454 66, 117, 133
MMP1455 ehaH putative transmembrane subunit of a hydrogenase 66, 133
MMP1456 ehaI hypothetical protein MMP1456 66, 117, 133
MMP1457 ehaJ energy conserving hydrogenase A integral membrane subunit 66, 133
MMP1458 ehaK hypothetical protein MMP1458 66, 133
MMP1459 ehaL hypothetical protein MMP1459 66, 117, 133
MMP1460 ehaM hypothetical protein MMP1460 66, 133
MMP1462 ehaO energy conserving hydrogenase A large subunit 66, 133
MMP1463 ehaP polyferredoxin 66, 133
MMP1467 ehaT hypothetical protein MMP1467 28, 129, 133
MMP1531 hypothetical protein MMP1531 8, 66
MMP1573 bioD dethiobiotin synthase 28, 106
MMP1645 aspartate/glutamate/uridylate kinase 4, 126
MMP1657 hypothetical protein MMP1657 21, 28
MMP1662 cbiF precorrin-4 C11-methyltransferase 66, 117
MMP1665 HEAT domain-containing protein 66, 117
MMP1698 hypothetical protein MMP1698 4, 8
RNA_17 tRNA-Pro2 Pro tRNA 4, 100
Unanno_23 None 4, 101
Unanno_27 None 4, 101
Unanno_51 None 4, 126
Unanno_59 None 28, 104, 133
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 MMP1303
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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