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 Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2513 to 2562 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1257 espin. [refseq;acc:nm_031475] Divided 219.354 224.7 1.02437
flotillin-1. [swissprot;acc:o75955] Subtracted 218.368 213.22 5.148
1258 cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Divided 219.354 224.7 1.02437
sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] Subtracted 218.368 213.22 5.148
1259 pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] Divided 219.354 224.7 1.02437
signal transducer and activator of transcription 5a. [swissprot;acc:p42229] Subtracted 222.546 227.673 5.127
1260 lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] Divided 219.354 224.7 1.02437
signal transducer and activator of transcription 5b. [swissprot;acc:p51692] Subtracted 222.544 227.667 5.123
1261 d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] Divided 219.354 224.7 1.02437
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Subtracted 163.24 168.359 5.119
1262 keratin associated protein 9.2. [refseq;acc:nm_031961] Divided 219.353 224.678 1.02428
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Subtracted 226.347 221.259 5.088
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] Divided 171.231 167.177 1.02425
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Subtracted 212.724 207.637 5.087
1264 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Divided 171.231 167.177 1.02425
1265 phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] Subtracted 212.724 207.637 5.087
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] Divided 171.231 167.177 1.02425
1266 mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Subtracted 217.635 212.575 5.06
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] Divided 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]
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Subtracted 217.634 212.576 5.058
1268 histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] 226.433 231.491
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Divided 171.231 167.177 1.02425
1269 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] Subtracted 226.433 231.491 5.058
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Divided 171.231 167.177 1.02425
1270 histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] Subtracted 226.433 231.491 5.058
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Divided 171.231 167.177 1.02425
1271 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Subtracted 245.532 240.483 5.049
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Divided 171.231 167.177 1.02425
1272 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Subtracted 217.624 212.584 5.04
1273 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Divided 171.231 167.177 1.02425
serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] Subtracted 218.439 213.436 5.003
1274 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] Divided 171.231 167.177 1.02425
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] Subtracted 218.44 213.439 5.001
1275 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Divided 171.231 167.177 1.02425
serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] Subtracted 218.441 213.441 5
1276 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Divided 171.231 167.177 1.02425
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] Subtracted 218.44 213.44 5
1277 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 250.854 255.842 4.988
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Divided 171.231 167.177 1.02425
1278 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Subtracted 228.409 223.475 4.934
sestrin 3. [swissprot;acc:p58005] Divided 218.368 213.219 1.02415
1279 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Subtracted 228.409 223.475 4.934
sestrin 2 (hi95). [swissprot;acc:p58004] Divided 218.368 213.219 1.02415
1280 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 213.22 1.02414
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Subtracted 228.409 223.475 4.934
1281 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Divided 218.368 213.22 1.02414
heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] Subtracted 228.409 223.475 4.934

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
- 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/