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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Filtered Gene Value Type Rank network_comparison description green Interaction Map Network Comparison Type red
Results: HTML CSV LaTeX Showing element 501 to 550 of 29840 in total
Filtered  : 0
Value Type  : Measured
Interaction Map  : High confidence
Rank
network_comparison
description
green
Network Comparison Type
red
251 1.13498 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 1079.38 Divided 1225.08
127.847 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] 142.417 Subtracted 270.264
252 1.13498 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 1079.38 Divided 1225.08
125.45 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 2164.92 Subtracted 2039.47
253 1.13498 espin. [refseq;acc:nm_031475] 1079.38 Divided 1225.07
125 hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] 681 Subtracted 556
254 1.13461 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 1495.66 Divided 1318.22
125 dc11 protein. [refseq;acc:nm_020186] 681 Subtracted 556
255 1.1346 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 1495.22 Divided 1317.84
124.74 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 2633.79 Subtracted 2509.05
256 1.13418 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 1079.77 Divided 1224.65
124.41 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 4091.59 Subtracted 3967.18
257 1.13358 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 759.896 Divided 861.401
124.174 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 612.604 Subtracted 488.43
258 1.13048 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 1337.54 Divided 1183.16
124.009 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 6.50325 Subtracted 130.512
259 1.1297 60s ribosomal protein l23a. [swissprot;acc:p29316] 1463.51 Divided 1295.49
121.769 myosin vi. [swissprot;acc:q9um54] 224.096 Subtracted 345.865
260 1.1296 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 2202 Divided 1949.36
120.26 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 1268.19 Subtracted 1388.45
261 1.12945 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 1463.55 Divided 1295.81
118.486 presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 86.9525 Subtracted 205.439
262 1.12926 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 676.971 Divided 764.479
117.701 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 723.75 Subtracted 606.049
263 1.1286 sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] 1633 Divided 1843
117.163 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] 615.233 Subtracted 498.07
264 1.12829 sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] 2957.12 Divided 3336.48
115.5 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 1721.76 Subtracted 1837.26
265 1.12375 60s ribosomal protein l9. [swissprot;acc:p32969] 1894.01 Divided 1685.44
109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 109 Subtracted 0
266 1.1235 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 1312.91 Divided 1475.05
108.21 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 1104.61 Subtracted 1212.82
267 1.1235 uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] 1312.91 Divided 1475.05
104.717 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 975.647 Subtracted 870.93
268 1.12346 far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] 538.094 Divided 604.529
101.505 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 759.896 Subtracted 861.401
269 1.12309 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 1367.83 Divided 1217.92
101.217 syntaxin 10 (syn10). [swissprot;acc:o60499] 17.6611 Subtracted 118.878
270 1.12309 ribosomal protein l10-like protein. [refseq;acc:nm_080746] 1367.88 Divided 1217.96
101 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 56 Subtracted 157
271 1.12278 histone h4. [swissprot;acc:p02304] 24446.3 Divided 21773.1
100.86 60s ribosomal protein l39. [swissprot;acc:p02404] 2923.92 Subtracted 3024.78
272 1.12261 60s ribosomal protein l15. [swissprot;acc:p39030] 753.793 Divided 846.216
100.257 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 650.724 Subtracted 750.981
273 1.1218 sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 1582.65 Divided 1410.81
99.867 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 758.411 Subtracted 658.544
274 1.12172 brain protein 16. [refseq;acc:nm_016458] 2418.14 Divided 2155.75
99.85 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 1591.6 Subtracted 1491.75
275 1.12172 swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] 804.725 Divided 717.401
97.48 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 2254.12 Subtracted 2156.64

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/