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 Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2463 to 2512 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1232 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Subtracted 209.649 204.406 5.243
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Divided 172.543 168.417 1.0245
1233 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] 212.724 207.637
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted 142.077 136.846 5.231
1234 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] Divided 212.724 207.637 1.0245
ubiquitin. [swissprot;acc:p02248] Subtracted 209.6 204.372 5.228
1235 coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] 177.432 182.647 5.215
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Divided 219.356 224.723 1.02447
1236 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 219.354 224.699 1.02437
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Subtracted 226.439 221.26 5.179
1237 keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] Divided 219.354 224.699 1.02437
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Subtracted 226.439 221.26 5.179
1238 keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Divided 219.354 224.699 1.02437
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Subtracted 226.439 221.26 5.179
1239 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Divided 219.354 224.699 1.02437
signal transducer and activator of transcription 4. [swissprot;acc:q14765] Subtracted 222.573 227.751 5.178
1240 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Divided 219.354 224.7 1.02437
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] Subtracted 222.574 227.752 5.178
1241 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Divided 219.354 224.7 1.02437
signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] Subtracted 222.573 227.75 5.177
1242 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Divided 219.354 224.7 1.02437
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Subtracted 162.055 156.884 5.171
1243 keratin associated protein 1.5. [refseq;acc:nm_031957] Divided 219.354 224.699 1.02437
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] Subtracted 222.569 227.739 5.17
1244 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Divided 219.354 224.7 1.02437
tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] Subtracted 206.774 211.936 5.162
1245 keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Divided 219.354 224.699 1.02437
tumor protein d52 (n8 protein). [swissprot;acc:p55327] Subtracted 206.771 211.926 5.155
1246 keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Divided 219.354 224.699 1.02437
sestrin 3. [swissprot;acc:p58005] Subtracted 218.368 213.219 5.149
1247 sestrin 2 (hi95). [swissprot;acc:p58004]
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Divided 219.354 224.7 1.02437
1248 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] Subtracted 218.368 213.22 5.148
keratin associated protein 4.4. [refseq;acc:nm_032524] Divided 219.354 224.699 1.02437
1249 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 224.7
cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Subtracted 218.368 213.22 5.148
1250 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Divided 219.354 224.7 1.02437
1251 integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Subtracted 218.368 213.22 5.148
1252 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] Divided 219.354 224.7 1.02437
1253 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Subtracted 218.368 213.22 5.148
ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] Divided 219.354 224.7 1.02437
1254 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Subtracted 218.368 213.22 5.148
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Divided 219.354 224.7 1.02437
1255 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Subtracted 218.368 213.22 5.148
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Divided 219.354 224.7 1.02437
1256 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Subtracted 218.368 213.22 5.148
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Divided 219.354 224.699 1.02437

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/