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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2058 to 2107 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1029 DDB1 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] Divided 222.364 215.535 1.03168
1030 PCCB 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]
RDH8 retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Subtracted 211.449 217.998 6.549
1031 ASNSD1 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 219.01 212.468 6.542
EMG1 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Divided 242.978 235.518 1.03167
1032 AGPAT2 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] 186.664 180.943 1.03162
ATP6V1A 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] Subtracted 219.01 212.468 6.542
1033 ASNS asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
TYR tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Divided 221.183 214.406 1.03161
1034 no value 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Subtracted 229.442 235.974 6.532
ESRRB steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Divided 186.551 180.837 1.0316
1035 MAGI2 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] 221.682 228.68 1.03157
RPS27L ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Subtracted 229.441 235.972 6.531
1036 COPB1 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Divided 171.341 176.746 1.03155
DLD dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] Subtracted 207.719 214.236 6.517
1037 GLRX3 thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] Divided 228.412 235.609 1.03151
NLK nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Subtracted 218.162 211.648 6.514
1038 no value 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] Divided 186.741 181.041 1.03148
ERC1 elks protein. [refseq;acc:nm_015064] Subtracted 218.162 211.648 6.514
1039 DLD dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] Divided 207.719 214.236 1.03137
PLEKHF2 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Subtracted 220.118 213.685 6.433
1040 CCT5 t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Divided 163.24 168.359 1.03136
SRD5A1 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] Subtracted 220.118 213.685 6.433
1041 HNRNPL heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Divided 186.774 181.099 1.03134
SRD5A2 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] Subtracted 220.118 213.685 6.433
1042 no value estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Divided 186.799 181.127 1.03132
WBP2 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Subtracted 216.901 210.485 6.416
1043 no value nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] 239.219 232.837 6.382
AGPAT3 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] Divided 187.834 182.137 1.03128
1044 DYNLT3 t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] 173.475 178.889 1.03121
FHL5 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] Subtracted 269.157 275.531 6.374
1045 CBS cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 205.632 199.266 6.366
FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Divided 115.817 119.432 1.03121
1046 MRE11A double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] 173.475 178.889
RHOC transforming protein rhoc (h9). [swissprot;acc:p08134] Subtracted 205.632 199.266 6.366
1047 ESRRA steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Divided 187.022 181.391 1.03104
TST thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Subtracted 205.632 199.266 6.366
1048 AGPAT4 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] Divided 187.96 182.308 1.031
MPST 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Subtracted 205.632 199.266 6.366
1049 no value adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Divided 211.449 217.998 1.03097
RHOA transforming protein rhoa (h12). [swissprot;acc:p06749] Subtracted 205.632 199.266 6.366
1050 BYSL bystin. [swissprot;acc:q13895] 239.505 233.185 6.32
HSD17B1 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] Divided 211.449 217.998 1.03097
1051 no value 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
ANXA11 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] Subtracted 219.673 213.378 6.295
1052 KARS lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] 220.291 226.584 6.293
RDH8 retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Divided 211.449 217.998 1.03097
1053 ANXA7 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] Subtracted 219.655 213.385 6.27
PSMA5 proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Divided 207.04 200.84 1.03087
1054 no value 60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 217.263 1.03082

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/