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 Gene description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2051 to 2100 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
red
green
network_comparison
1026 hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] HAO1 Subtracted 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
1038 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] no value 186.741 181.041 1.03148
elks protein. [refseq;acc:nm_015064] ERC1 Subtracted 218.162 211.648 6.514
1039 dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] DLD Divided 207.719 214.236 1.03137
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] PLEKHF2 Subtracted 220.118 213.685 6.433
1040 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] SRD5A1
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] CCT5 Divided 163.24 168.359 1.03136
1041 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] SRD5A2 Subtracted 220.118 213.685 6.433
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] HNRNPL Divided 186.774 181.099 1.03134
1042 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] no value 186.799 181.127 1.03132
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] WBP2 Subtracted 216.901 210.485 6.416
1043 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] AGPAT3 Divided 187.834 182.137 1.03128
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] no value Subtracted 239.219 232.837 6.382
1044 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] FHL5 269.157 275.531 6.374
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] DYNLT3 Divided 173.475 178.889 1.03121
1045 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] CBS Subtracted 205.632 199.266 6.366
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] FIP1L1 Divided 115.817 119.432 1.03121
1046 double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] MRE11A 173.475 178.889
transforming protein rhoc (h9). [swissprot;acc:p08134] RHOC Subtracted 205.632 199.266 6.366
1047 steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] ESRRA Divided 187.022 181.391 1.03104
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] TST Subtracted 205.632 199.266 6.366
1048 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] AGPAT4 Divided 187.96 182.308 1.031
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST Subtracted 205.632 199.266 6.366
1049 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] no value Divided 211.449 217.998 1.03097
transforming protein rhoa (h12). [swissprot;acc:p06749] RHOA Subtracted 205.632 199.266 6.366
1050 bystin. [swissprot;acc:q13895] BYSL 239.505 233.185 6.32
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 Divided 211.449 217.998 1.03097

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/