Organism : Methanococcus maripaludis S2 | Module List :
MMP0736

PRC-barrel domain-containing protein

CircVis
Functional Annotations (1)
Function System
Uncharacterized conserved protein cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0736
(Mouseover regulator name to see its description)

MMP0736 is regulated by 17 influences and regulates 0 modules.
Regulators for MMP0736 (17)
Regulator Module Operator
H2 8 ef
MMP0217
MMP1646
8 combiner
MMP0465
Formate
8 combiner
MMP1210
MMP1646
8 combiner
MMP1304 8 tf
MMP0031
MMP1704
38 combiner
MMP0041
MMP0568
38 combiner
MMP0480
MMP0568
38 combiner
MMP0568 38 tf
MMP0568
MMP1100
38 combiner
MMP0719
MMP1646
38 combiner
MMP1275 38 tf
MMP1499
MMP1646
38 combiner
MMP0018
MMP1100
19 combiner
MMP0052
Formate
19 combiner
MMP0097
Formate
19 combiner
MMP1100 19 tf

Warning: MMP0736 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
677 6.30e-02 cccgcaGgTTCaactcccccTccc
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678 8.30e-01 aGGTGATTTT
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699 7.40e+01 TaTaTaaa.tTTtctAtTtga.tt
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700 1.10e+04 GCCGGA
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737 3.90e+03 CCCTCcCc
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738 6.50e+03 ACCACC
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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 MMP0736

MMP0736 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized conserved protein cog/ cog
Module neighborhood information for MMP0736

MMP0736 has total of 109 gene neighbors in modules 8, 19, 38
Gene neighbors (109)
Gene Common Name Description Module membership
Antisense_27 None 19, 50
MMP0025 hypothetical protein MMP0025 8, 52
MMP0041 tfb transcription initiation factor IIB 19, 160
MMP0042 H/ACA RNA-protein complex component Gar1 19, 108
MMP0059 hypothetical protein MMP0059 8, 58, 64
MMP0061 aIF6 translation initiation factor IF-6 8, 61, 96, 138
MMP0093 50S ribosomal protein L21e 8, 11, 20
MMP0094 putative pseudouridylate synthase 8, 11
MMP0103 pyridoxal biosynthesis lyase PdxS 8, 27, 77
MMP0116 argC N-acetyl-gamma-glutamyl-phosphate reductase 8, 51
MMP0127 hmd H(2)-dependent methylenetetrahydromethanopterin dehydrogenase 8, 77
MMP0183 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase 8, 70
MMP0221 putP sodium/proline symporter 29, 38
MMP0233 hypothetical protein MMP0233 38, 115
MMP0242 hypothetical protein MMP0242 8, 39, 96
MMP0243 hypothetical protein MMP0243 4, 25, 38
MMP0278 putative CBS domain-containing signal transduction protein 19, 90
MMP0290 nac nascent polypeptide-associated complex protein 8, 78
MMP0309 DsrE family protein 8, 78
MMP0344 hypothetical protein MMP0344 19, 90
MMP0351 aspB-like1 DegT/DnrJ/EryC1/StrS aminotransferase 38, 80
MMP0352 putative oxidoreductase 38, 80, 162
MMP0371 hypothetical protein MMP0371 8, 70
MMP0382 putative ATPase RIL 8, 70, 78
MMP0386 HMmA histone A 38, 126
MMP0405 gch3 GTP cyclohydrolase III 19, 92
MMP0407 hypothetical protein MMP0407 8, 19, 89
MMP0414 thrS threonyl-tRNA synthetase 8, 81, 112
MMP0419 sodium:neurotransmitter symporter 24, 38
MMP0539 leuB multifunctional 3-isopropylmalate dehydrogenase/D-malate dehydrogenase 7, 8
MMP0540 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 8, 112, 143
MMP0597 flpA fibrillarin 8, 16, 81
MMP0629 hypothetical protein MMP0629 8, 39
MMP0632 ATP/GTP-binding motif-containing protein 19, 115
MMP0645 mdh malate dehydrogenase 8, 39, 136
MMP0650 ilvB acetolactate synthase catalytic subunit 8, 39
MMP0651 ilvH acetolactate synthase 3 regulatory subunit 8, 39
MMP0655 hypothetical protein MMP0655 24, 38, 52
MMP0657 hypothetical protein MMP0657 8, 29, 96
MMP0679 Na+/H+ antiporter-like protein 24, 38
MMP0687 tpiA triosephosphate isomerase 8, 13
MMP0689 xanthine/uracil permease family protein 38, 115
MMP0697 leuS leucyl-tRNA synthetase 8, 143
MMP0701 hypothetical protein MMP0701 38, 162
MMP0702 hypothetical protein MMP0702 24, 38, 162
MMP0704 ParA type ATPase 8, 78, 112
MMP0736 PRC-barrel domain-containing protein 8, 19, 38
MMP0737 L-aspartate dehydrogenase 8, 38
MMP0762 hypothetical protein MMP0762 19, 43
MMP0816 seryl-tRNA synthetase-like protein 8, 70
MMP0839 hypothetical protein MMP0839 29, 38
MMP0840 TetR family transcriptional regulator 29, 38
MMP0898 cellulose-binding protein 8, 70
MMP0910 hypothetical protein MMP0910 38, 86, 122
MMP0911 iron-sulfur flavoprotein 38, 80
MMP0946 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B 8, 81, 96
MMP0965 formylmethanofuran dehydrogenase subunit E-like protein 8, 39, 136
MMP0971 purB adenylosuccinate lyase 8, 11
MMP1021 hypothetical protein MMP1021 8, 21
MMP1023 TetR family transcriptional regulator 8, 21, 78
MMP1067 succinate dehydrogenase/fumarate reductase iron-sulfur subunit 19, 123
MMP1070 hypothetical protein MMP1070 8, 15
MMP1094 ppsA phosphoenolpyruvate synthase 38, 80
MMP1103 hypothetical protein MMP1103 14, 38
MMP1130 hypothetical protein MMP1130 4, 38
MMP1213 hypothetical protein MMP1213 8, 89
MMP1223 hypothetical protein MMP1223 19, 123
MMP1244 fwdH tungsten containing formylmethanofuran dehydrogenase subunit H 19, 89
MMP1245 fwdF tungsten containing formylmethanofuran dehydrogenase subunit F 19, 89
MMP1246 fwdG tungsten containing formylmethanofuran dehydrogenase subunit G 19, 89
MMP1247 fwdD tungsten containing formylmethanofuran dehydrogenase subunit D 19, 89
MMP1248 fwdA tungsten containing formylmethanofuran dehydrogenase subunit A 19, 89
MMP1249 fwdC tungsten containing formylmethanofuran dehydrogenase subunit C 19, 89
MMP1257 NERD domain-containing protein 19, 43
MMP1258 hemB delta-aminolevulinic acid dehydratase 19, 124
MMP1270 bifunctional hexulose-6-phosphate synthase/ribonuclease regulator 24, 38
MMP1308 tal putative translaldolase 8, 16, 112
MMP1321 rps11p 30S ribosomal protein S11P 8, 105, 118
MMP1352 ribulose-1,5-biphosphate synthetase 7, 8, 78
MMP1471 hypothetical protein MMP1471 38, 115
MMP1475 hypothetical protein MMP1475 19, 50
MMP1511 amino acid carrier protein 19, 92
MMP1512 alr alanine racemase 8, 21
MMP1513 ald alanine dehydrogenase 8, 21
MMP1527 aspartate aminotransferase 8, 21
MMP1531 hypothetical protein MMP1531 8, 66
MMP1541 hypothetical protein MMP1541 24, 38
MMP1555 mcrB methyl-coenzyme M reductase I subunit beta 19, 89
MMP1556 mcrD methyl-coenzyme M reductase I, protein D 19, 89
MMP1557 mcrC methyl coenzyme M reductase I, protein C 19, 89
MMP1558 mcrG methyl-coenzyme M reductase I subunit gamma 19, 89
MMP1559 mcrA methyl-coenzyme M reductase I subunit alpha 19, 89
MMP1586 hypothetical protein MMP1586 19, 100
MMP1588 serA D-3-phosphoglycerate dehydrogenase 7, 8, 27, 77
MMP1609 ftr formylmethanofuran--tetrahydromethanopterin formyltransferase 19, 89
MMP1610 hypothetical protein MMP1610 19, 139
MMP1637 hypothetical protein MMP1637 13, 19
MMP1643 hypothetical protein MMP1643 35, 38
MMP1656 glutamine amidotransferase subunit PdxT 8, 137
MMP1698 hypothetical protein MMP1698 4, 8
MMP1705 creatininase 8, 11, 20
MMP1712 LysR family transcriptional regulator 19, 106
MMP1714 roadblock/LC7 family protein 38, 162
MMP1715 small GTP-binding protein 38, 162
MMP1716 hmdII H(2)-dependent methylenetetrahydromethanopterin dehydrogenase-like protein 38, 162
Unanno_15 None 8, 44
Unanno_17 None 8, 126
Unanno_45 None 9, 38
Unanno_8 None 8, 78
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 MMP0736
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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