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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2618 to 2667 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1309 VBP1 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Divided 226.439 221.26 1.02341
1310 FANCL phd finger protein 9. [refseq;acc:nm_018062] Subtracted 216.772 221.594 4.822
PFDN2 prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Divided 226.439 221.26 1.02341
1311 SOLH small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] Subtracted 216.772 221.594 4.822
UXT uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Divided 226.439 221.26 1.02341
1312 GALK2 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Subtracted 215.162 210.412 4.75
RAD50 rad50 homolog isoform 1. [refseq;acc:nm_005732] Divided 199.739 204.407 1.02337
1313 no value galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Subtracted 215.162 210.412 4.75
STAT3 signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] Divided 222.573 227.75 1.02326
1314 GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Subtracted 215.162 210.412 4.75
STAT4 signal transducer and activator of transcription 4. [swissprot;acc:q14765] Divided 222.573 227.751 1.02326
1315 STAT1 signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] 222.574 227.752
ZIC1 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Subtracted 218.569 213.832 4.737
1316 STAT6 signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] Divided 222.569 227.739 1.02323
ZIC3 zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Subtracted 218.572 213.841 4.731
1317 CENPJ centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Divided 206.773 202.105 1.0231
ZIC2 zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Subtracted 218.574 213.847 4.727
1318 CREB5 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 218.591 213.899 4.692
STAT5A signal transducer and activator of transcription 5a. [swissprot;acc:p42229] Divided 222.546 227.673 1.02304
1319 CENPJ centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Subtracted 206.773 202.105 4.668
GYS1 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Divided 159.75 156.153 1.02304
1320 RAD50 rad50 homolog isoform 1. [refseq;acc:nm_005732] Subtracted 199.739 204.407 4.668
STAT5B signal transducer and activator of transcription 5b. [swissprot;acc:p51692] Divided 222.544 227.667 1.02302
1321 CDC25C m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Subtracted 259.439 254.797 4.642
DIMT1L probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Divided 226.347 221.259 1.023
1322 no value endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 159.86 156.275 1.02294
SOCS1 suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Subtracted 216.542 211.908 4.634
1323 GMFG glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
NCK2 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Divided 205.225 200.625 1.02293
1324 ASCC2 asc-1 complex subunit p100. [refseq;acc:nm_032204] Subtracted 216.542 211.908 4.634
GYS2 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Divided 159.993 156.421 1.02284
1325 FKBP1A fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Subtracted 216.542 211.908 4.634
WRNIP1 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Divided 217.133 212.289 1.02282
1326 CSMD1 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 218.509 213.648 1.02275
USF1 upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Subtracted 214.987 210.359 4.628
1327 EYA3 eyes absent homolog 3. [swissprot;acc:q99504] 218.537 213.91 4.627
ZIC4 zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Divided 218.509 213.648 1.02275
1328 RCAN2 calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] 213.649
USF2 upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Subtracted 214.971 210.354 4.617
1329 no value dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Divided 218.509 213.648 1.02275
NCK2 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Subtracted 205.225 200.625 4.6
1330 RCAN1 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] Divided 218.508 213.648 1.02275
SALL2 sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Subtracted 218.471 213.876 4.595
1331 RCAN3 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] Divided 218.509 213.649 1.02275
RERE arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] Subtracted 218.47 213.875 4.595
1332 ATN1 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] 218.471 213.876
OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Divided 220.681 215.78 1.02271
1333 no value dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Subtracted 218.47 213.875 4.595
MRPL34 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] Divided 220.681 215.78 1.02271
1334 PRAF2 jm4 protein. [refseq;acc:nm_007213] 199.643 204.163 1.02264

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/