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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 2630 to 2679 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
1315 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Subtracted 218.569 4.737 213.832
1316 signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] Divided 222.569 1.02323 227.739
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Subtracted 218.572 4.731 213.841
1317 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Divided 206.773 1.0231 202.105
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Subtracted 218.574 4.727 213.847
1318 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 218.591 4.692 213.899
signal transducer and activator of transcription 5a. [swissprot;acc:p42229] Divided 222.546 1.02304 227.673
1319 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Subtracted 206.773 4.668 202.105
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Divided 159.75 1.02304 156.153
1320 rad50 homolog isoform 1. [refseq;acc:nm_005732] Subtracted 199.739 4.668 204.407
signal transducer and activator of transcription 5b. [swissprot;acc:p51692] Divided 222.544 1.02302 227.667
1321 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Subtracted 259.439 4.642 254.797
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Divided 226.347 1.023 221.259
1322 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 159.86 1.02294 156.275
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 4.634 211.908
1323 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Divided 205.225 1.02293 200.625
glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Subtracted 216.542 4.634 211.908
1324 asc-1 complex subunit p100. [refseq;acc:nm_032204]
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Divided 159.993 1.02284 156.421
1325 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 4.634 211.908
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Divided 217.133 1.02282 212.289
1326 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 218.509 1.02275 213.648
upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Subtracted 214.987 4.628 210.359
1327 eyes absent homolog 3. [swissprot;acc:q99504] 218.537 4.627 213.91
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Divided 218.509 1.02275 213.648
1328 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
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Subtracted 214.971 4.617 210.354
1329 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] 205.225 4.6 200.625
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Divided 218.509 1.02275 213.648
1330 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 218.508
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Subtracted 218.471 4.595 213.876
1331 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 218.47 213.875
calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] Divided 218.509 1.02275 213.649
1332 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Subtracted 218.471 4.595 213.876
cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Divided 220.681 1.02271 215.78
1333 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Subtracted 218.47 4.595 213.875
1334 jm4 protein. [refseq;acc:nm_007213] Divided 199.643 1.02264 204.163
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Subtracted 218.47 4.595 213.875
1335 cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407] Divided 199.771 1.02261 204.287
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Subtracted 218.471 4.595 213.876
1336 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] 218.47 213.875
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Divided 215.162 1.02257 210.412
1337 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Subtracted 218.47 4.595 213.875
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Divided 215.162 1.02257 210.412
1338 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Subtracted 218.47 4.595 213.875
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Divided 215.162 1.02257 210.412
1339 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Subtracted 218.471 4.595 213.876
epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Divided 205.204 1.02239 200.71
1340 histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] 226.433 1.02234 231.491

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/