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 5758 to 5807 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1440 megf10 protein. [refseq;acc:nm_032446] Rooted 60.5986 62.9711 1.03915
mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] Ranked 225.039 229.573 1.02015
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Measured 6522.96 7023.77 1.07678
1441 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] Rooted 60.5976 62.9699 1.03915
fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265] Ranked 225.039 229.573 1.02015
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] Measured 6216.12 6693.38 1.07678
uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Squared 23913 26757.8 1.11896
1442 e-1 enzyme. [refseq;acc:nm_021204] Rooted 66.6168 69.2218 1.0391
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Ranked 225.039 229.573 1.02015
myosin vi. [swissprot;acc:q9um54] Squared 23913 26757.8 1.11896
proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] Measured 6216.13 6693.13 1.07674
1443 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] Rooted 60.5585 62.9256 1.03909
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Ranked 203.908 207.998 1.02006
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Measured 5450.9 5869.07 1.07672
transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] Squared 21029.4 23523.8 1.11861
1444 glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] Ranked 203.908 207.998 1.02006
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Measured 5450.9 5869.07 1.07672
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Squared 21029.4 23523.8 1.11861
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Rooted 99.8942 96.137 1.03908
1445 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Measured 5117.85 5510.45 1.07671
cyclin c. [swissprot;acc:p24863] Rooted 63.4594 65.9327 1.03897
mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Squared 17710.1 19805.6 1.11832
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Ranked 134.233 136.922 1.02003
1446 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Squared 30323.4 33911.1 1.11831
heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] Ranked 221.817 226.23 1.01989
lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Rooted 60.3013 62.6496 1.03894
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Measured 5117.85 5510.45 1.07671
1447 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Ranked 250.854 255.842 1.01988
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Measured 5117.85 5510.45 1.07671
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Rooted 62.5225 64.9556 1.03892
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Squared 15810.1 17678.6 1.11818
1448 ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Rooted 62.5225 64.9556 1.03892
caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Ranked 226.532 222.117 1.01988
dpy-30-like protein. [swissprot;acc:q9c005] Measured 5602.01 6031.05 1.07659
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Squared 20900.3 23366.9 1.11802
1449 lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Rooted 62.5225 64.9556 1.03892
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Measured 5602.01 6031.05 1.07659
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Squared 15509.6 17339.5 1.11798
transportin-sr; importin 12. [refseq;acc:nm_012470] Ranked 225.305 229.766 1.0198
1450 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 221.804 226.194 1.01979
gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Measured 5602.01 6031.05 1.07659
iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] Squared 49941.4 44680.1 1.11775
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Rooted 62.5225 64.9556 1.03892
1451 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Squared 26952.5 30122.8 1.11763
my016 protein. [sptrembl;acc:q9h3k6] Ranked 224.755 229.2 1.01978
neighbor of cox4. [swissprot;acc:o43402] Measured 5602.01 6031.05 1.07659
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Rooted 62.5225 64.9556 1.03892
1452 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Ranked 160.381 163.554 1.01978
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Squared 26952.5 30122.8 1.11763
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Measured 5602.01 6031.05 1.07659

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/