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 Hugo Value Type description 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
Hugo
Value Type
description
red
green
network_comparison
1440 OCRL Squared inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] 23913 26757.8 1.11896
PEX14 Measured peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] 6522.96 7023.77 1.07678
SMAD4 Ranked mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] 225.039 229.573 1.02015
1441 ADD2 Rooted beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 60.5976 62.9699 1.03915
FADS2 Ranked fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265] 225.039 229.573 1.02015
PSMA7 Measured proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] 6216.12 6693.38 1.07678
RAD23B Squared uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] 23913 26757.8 1.11896
1442 no value Ranked fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 225.039 229.573 1.02015
Squared myosin vi. [swissprot;acc:q9um54] 23913 26757.8 1.11896
ENOPH1 Rooted e-1 enzyme. [refseq;acc:nm_021204] 66.6168 69.2218 1.0391
PSMA8 Measured proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] 6216.13 6693.13 1.07674
1443 ADD1 Rooted alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 60.5585 62.9256 1.03909
GLUD2 Ranked glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 203.908 207.998 1.02006
KHK Measured ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] 5450.9 5869.07 1.07672
TCEA2 Squared 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] 21029.4 23523.8 1.11861
1444 no value Measured purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 5450.9 5869.07 1.07672
Squared transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 21029.4 23523.8 1.11861
GLUDP5 Ranked glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] 203.908 207.998 1.02006
TP53BP2 Rooted tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 99.8942 96.137 1.03908
1445 CCNC cyclin c. [swissprot;acc:p24863] 63.4594 65.9327 1.03897
CD109 Measured cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] 5117.85 5510.45 1.07671
MRPL27 Squared mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] 17710.1 19805.6 1.11832
PCF11 Ranked pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 134.233 136.922 1.02003
1446 CCDC85B Squared delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 30323.4 33911.1 1.11831
HSPB1 Ranked 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] 221.817 226.23 1.01989
LIN7A Rooted lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] 60.3013 62.6496 1.03894
PIN1 Measured peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] 5117.85 5510.45 1.07671
1447 IRX4 iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413]
LIPF Rooted triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] 62.5225 64.9556 1.03892
MPHOSPH10 Squared u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 15810.1 17678.6 1.11818
POLE3 Ranked dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 250.854 255.842 1.01988
1448 no value Measured dpy-30-like protein. [swissprot;acc:q9c005] 5602.01 6031.05 1.07659
HEMK1 Squared hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 20900.3 23366.9 1.11802
LIPM Rooted ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] 62.5225 64.9556 1.03892
ZMPSTE24 Ranked 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] 226.532 222.117 1.01988
1449 LIPA Rooted 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] 62.5225 64.9556 1.03892
RAB11FIP1 Measured rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] 5602.01 6031.05 1.07659
TBL3 Squared transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] 15509.6 17339.5 1.11798
TNPO3 Ranked transportin-sr; importin 12. [refseq;acc:nm_012470] 225.305 229.766 1.0198
1450 ACO1 Squared 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] 49941.4 44680.1 1.11775
HSPB8 Ranked alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 221.804 226.194 1.01979
RAB11FIP5 Measured gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] 5602.01 6031.05 1.07659
SARS2 Rooted seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] 62.5225 64.9556 1.03892
1451 BOLA2B Ranked my016 protein. [sptrembl;acc:q9h3k6] 224.755 229.2 1.01978
COX4NB Measured neighbor of cox4. [swissprot;acc:o43402] 5602.01 6031.05 1.07659
MAD2L2 Squared mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] 26952.5 30122.8 1.11763
SARS Rooted seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] 62.5225 64.9556 1.03892
1452 no value Ranked cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 160.381 163.554 1.01978
Squared mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 26952.5 30122.8 1.11763
C14orf122 Measured protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] 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
- 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/