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 Network Comparison Type description Hugo Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2501 to 2550 of 8289 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Interaction Map
red
green
network_comparison
1251 integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] ILK High confidence 219.354 224.7 1.02437
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] ZIC2 Low confidence 204.937 200.402 1.02263
1252 elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] ELAVL2 202.261 197.788 1.02262
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] STARD4 High confidence 219.354 224.7 1.02437
1253 ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] RSU1
syntaxin 18. [swissprot;acc:q9p2w9] STX18 Low confidence 204.026 199.515 1.02261
1254 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] AIG1
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] G3BP1 High confidence 219.354 224.7 1.02437
1255 mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] PBLD Low confidence 185.205 181.112 1.0226
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] G3BP2 High confidence 219.354 224.7 1.02437
1256 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] no value 224.699
serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] ACVR1B Low confidence 204.05 199.543 1.02259
1257 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] ACVR1C
espin. [refseq;acc:nm_031475] ESPNP High confidence 219.354 224.7 1.02437
1258 cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] CYP2D6
tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] TGFBR1 Low confidence 204.05 199.545 1.02258
1259 pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] PLEKHC1 High confidence 219.354 224.7 1.02437
smp3 mannosyltransferase. [refseq;acc:nm_025163] PIGZ Low confidence 202.715 198.24 1.02257
1260 lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] LIMS2 High confidence 219.354 224.7 1.02437
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] COX10 Low confidence 199.952 195.538 1.02257
1261 d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] DRD4 High confidence 219.354 224.7 1.02437
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] no value Low confidence 203.503 199.013 1.02256
1262 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] KATNB1 203.846 199.351 1.02255
keratin associated protein 9.2. [refseq;acc:nm_031961] KRTAP9-8 High confidence 219.353 224.678 1.02428
1263 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] MAPK11 171.231 167.177 1.02425
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] SNW1 Low confidence 196.724 192.389 1.02253
1264 ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907] RAB11B 203.934 199.445 1.02251
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] SPHK1 High confidence 171.231 167.177 1.02425
1265 kccr13l. [refseq;acc:nm_139179] DAGLB Low confidence 203.303 198.827 1.02251
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] DPAGT1 High confidence 171.231 167.177 1.02425
1266 nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] FDXR Low confidence 201.264 196.834 1.02251
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] DLC1 High confidence 171.231 167.177 1.02425
1267 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] MAPKAPK2
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] HIST1H2BA Low confidence 203.672 199.189 1.02251
1268 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] HARS2 192.905 188.658
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] CHRNA6 High confidence 171.231 167.177 1.02425
1269 ectonucleoside triphosphate diphosphohydrolase 6 (ec 3.6.1.6) (ntpdase6) (cd39 antigen-like 2). [swissprot;acc:o75354] no value Low confidence 196.818 192.485 1.02251
nitrogen fixation cluster-like. [refseq;acc:nm_014301] ISCU High confidence 171.231 167.177 1.02425
1270 cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] CYP2D6 Low confidence 201.858 197.415 1.02251
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] STARD13 High confidence 171.231 167.177 1.02425
1271 histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] HARS Low confidence 192.956 188.71 1.0225
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] STARD8 High confidence 171.231 167.177 1.02425
1272 ceramide glucosyltransferase (ec 2.4.1.80) (glucosylceramide synthase) (gcs) (udp-glucose:n-acylsphingosine d-glucosyltransferase) (glct-1). [swissprot;acc:q16739] UGCG Low confidence 192.933 188.687 1.0225
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] CHRNA2 High confidence 171.231 167.177 1.02425
1273 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] MAPKAPK3
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] PTPN2 Low confidence 200.744 196.329 1.02249
1274 cryptochrome 1 (photolyase-like). [refseq;acc:nm_004075] CRY1 193.539 189.282
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] MAPK14 High confidence 171.231 167.177 1.02425
1275 histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] HIST2H2BA Low confidence 203.671 199.194 1.02248
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] CHRNA4 High confidence 171.231 167.177 1.02425

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/