Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2025 to 2074 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
red
green
network_comparison
1013 protein bap28. [swissprot;acc:q9h583] HEATR1 Divided 244.312 236.647 1.03239
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] TOE1 Subtracted 217.365 210.558 6.807
1014 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] AATF Divided 243.045 235.422 1.03238
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] KPNA3 Subtracted 217.361 210.554 6.807
1015 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] MAGI1 Divided 221.73 228.906 1.03236
exocyst complex component sec6. [swissprot;acc:o60645] EXOC3 Subtracted 207.186 200.398 6.788
1016 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] KPNA4 Divided 217.369 210.561 1.03233
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] TYR Subtracted 221.183 214.406 6.777
1017 succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] SUCLG1 211.908 218.627 6.719
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] TOE1 Divided 217.365 210.558 1.03233
1018 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] KPNA3 217.361 210.554
succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] SUCLA2 Subtracted 211.908 218.627 6.719
1019 60s ribosomal protein l21. [swissprot;acc:p46778] no value 223.958 217.263 6.695
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] TYRL Divided 221.302 214.409 1.03215
1020 dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] DCT 221.28 1.03205
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] no value Subtracted 226.218 232.88 6.662
1021 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] TYRP1 Divided 221.278 214.409 1.03204
block 23. [sptrembl;acc:q8nhw5] no value Subtracted 226.205 232.858 6.653
1022 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] RPLP0 226.203 232.855 6.652
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] CBS Divided 205.632 199.266 1.03195
1023 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] BLOC1S1 Subtracted 202.027 195.386 6.641
transforming protein rhoc (h9). [swissprot;acc:p08134] RHOC Divided 205.632 199.266 1.03195
1024 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] DPM1 Subtracted 203.381 196.76 6.621
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] TST Divided 205.632 199.266 1.03195
1025 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST
40s ribosomal protein s30. [swissprot;acc:q05472] FAU Subtracted 223.44 216.875 6.565
1026 hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] HAO1 231.922 238.486 6.564
transforming protein rhoa (h12). [swissprot;acc:p06749] RHOA Divided 205.632 199.266 1.03195
1027 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] no value Subtracted 211.449 217.998 6.549
succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] SUCLG1 Divided 211.908 218.627 1.03171
1028 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] HSD17B1 Subtracted 211.449 217.998 6.549
succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] SUCLA2 Divided 211.908 218.627 1.03171
1029 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] no value Subtracted 211.449 217.998 6.549
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] DDB1 Divided 222.364 215.535 1.03168
1030 propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] PCCB
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] RDH8 Subtracted 211.449 217.998 6.549
1031 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] ASNSD1 219.01 212.468 6.542
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] EMG1 Divided 242.978 235.518 1.03167
1032 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] AGPAT2 186.664 180.943 1.03162
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] ATP6V1A Subtracted 219.01 212.468 6.542
1033 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] ASNS
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] TYR Divided 221.183 214.406 1.03161
1034 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] no value Subtracted 229.442 235.974 6.532
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] ESRRB Divided 186.551 180.837 1.0316
1035 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] MAGI2 221.682 228.68 1.03157
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] RPS27L Subtracted 229.441 235.972 6.531
1036 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] COPB1 Divided 171.341 176.746 1.03155
dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] DLD Subtracted 207.719 214.236 6.517
1037 nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] NLK 218.162 211.648 6.514
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] GLRX3 Divided 228.412 235.609 1.03151

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the HGNC identifier if it exists
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/