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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2462 to 2511 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1231 SDHB succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] Subtracted 207.931 213.175 5.244
1232 no value alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 209.649 204.406 5.243
PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Divided 172.543 168.417 1.0245
1233 no value 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
SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted 142.077 136.846 5.231
1234 PGAM2 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
UBB ubiquitin. [swissprot;acc:p02248] Subtracted 209.6 204.372 5.228
1235 no value keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Divided 219.356 224.723 1.02447
COPA coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Subtracted 177.432 182.647 5.215
1236 no value keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Divided 219.354 224.699 1.02437
VBP1 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 no value keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] Divided 219.354 224.699 1.02437
PFDN2 prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Subtracted 226.439 221.26 5.179
1238 no value keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Divided 219.354 224.699 1.02437
UXT uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Subtracted 226.439 221.26 5.179
1239 no value keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Divided 219.354 224.699 1.02437
STAT4 signal transducer and activator of transcription 4. [swissprot;acc:q14765] Subtracted 222.573 227.751 5.178
1240 no value keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Divided 219.354 224.7 1.02437
STAT1 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 no value keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Divided 219.354 224.7 1.02437
STAT3 signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] Subtracted 222.573 227.75 5.177
1242 no value keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Divided 219.354 224.7 1.02437
RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Subtracted 162.055 156.884 5.171
1243 no value keratin associated protein 1.5. [refseq;acc:nm_031957] Divided 219.354 224.699 1.02437
STAT6 signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] Subtracted 222.569 227.739 5.17
1244 STARD6 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Divided 219.354 224.7 1.02437
TPD52L1 tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] Subtracted 206.774 211.936 5.162
1245 KRTAP5-8 keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Divided 219.354 224.699 1.02437
TPD52 tumor protein d52 (n8 protein). [swissprot;acc:p55327] Subtracted 206.771 211.926 5.155
1246 no value keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Divided 219.354 224.699 1.02437
SESN3 sestrin 3. [swissprot;acc:p58005] Subtracted 218.368 213.219 5.149
1247 SESN2 sestrin 2 (hi95). [swissprot;acc:p58004]
STARD5 star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Divided 219.354 224.7 1.02437
1248 CYP4A11 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
KRTAP4-4 keratin associated protein 4.4. [refseq;acc:nm_032524] Divided 219.354 224.699 1.02437
1249 no value alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 224.7
CYP4F3 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 CYP4F8 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]
LIMS1 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 CYP4X1 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Subtracted 218.368 213.22 5.148
ILK integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] Divided 219.354 224.7 1.02437
1252 CYP4F12 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Subtracted 218.368 213.22 5.148
STARD4 star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] Divided 219.354 224.7 1.02437
1253 CYP4F2 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
RSU1 ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] Divided 219.354 224.7 1.02437
1254 CYP4F11 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Subtracted 218.368 213.22 5.148
G3BP1 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 CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Subtracted 218.368 213.22 5.148
G3BP2 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 no value keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 224.699

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/