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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2430 to 2479 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1215 PPIE peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Subtracted 174.387 179.697 5.31
1216 COPZ2 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
ZMIZ1 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Divided 218.269 212.918 1.02513
1217 HAS2 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Subtracted 221.093 226.399 5.306
QRSL1 glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Divided 211.959 217.258 1.025
1218 FAAH fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519]
HAS1 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Subtracted 221.093 226.399 5.306
1219 COTL1 coactosin-like protein. [swissprot;acc:q14019] Divided 211.959 217.258 1.025
HAS3 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Subtracted 221.093 226.399 5.306
1220 QRSL1 glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 211.959 217.258 5.299
UNG uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Divided 1.025
1221 FAAH fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Subtracted 5.299
PET112L probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Divided 1.025
1222 COTL1 coactosin-like protein. [swissprot;acc:q14019] Subtracted 5.299
TPD52L1 tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] Divided 206.774 211.936 1.02496
1223 TPD52 tumor protein d52 (n8 protein). [swissprot;acc:p55327] 206.771 211.926 1.02493
UNG uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Subtracted 211.959 217.258 5.299
1224 FPGS folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Divided 225.906 231.524 1.02487
PET112L probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Subtracted 211.959 217.258 5.299
1225 IL4I1 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] 219.55 214.288 5.262
UBE2E1 ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Divided 166.846 170.989 1.02483
1226 FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Subtracted 191.139 185.882 5.257
UBE2E4P ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Divided 166.846 170.989 1.02483
1227 GCLM glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] Subtracted 213.079 218.325 5.246
PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Divided 172.365 168.219 1.02465
1228 GCLC glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] Subtracted 213.079 218.325 5.246
GCLM glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] Divided 1.02462
1229 no value integral membrane protein cii-3b. [sptrembl;acc:o75609] Subtracted 207.646 212.891 5.245
GCLC glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] Divided 213.079 218.325 1.02462
1230 IL4I1 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] 219.55 214.288 1.02456
SDHC succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] Subtracted 207.644 212.888 5.244
1231 PGAM4 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Divided 212.724 207.637 1.0245
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

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/