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 Interaction Map Network Comparison Type Filtered red green network_comparison
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
green
network_comparison
1315 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Subtracted 218.569 213.832 4.737
1316 signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] Divided 222.569 227.739 1.02323
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Subtracted 218.572 213.841 4.731
1317 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
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Subtracted 218.574 213.847 4.727
1318 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 218.591 213.899 4.692
signal transducer and activator of transcription 5a. [swissprot;acc:p42229] Divided 222.546 227.673 1.02304
1319 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
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Divided 159.75 156.153 1.02304
1320 rad50 homolog isoform 1. [refseq;acc:nm_005732] Subtracted 199.739 204.407 4.668
signal transducer and activator of transcription 5b. [swissprot;acc:p51692] Divided 222.544 227.667 1.02302
1321 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Subtracted 259.439 254.797 4.642
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 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 159.86 156.275 1.02294
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 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
glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Subtracted 216.542 211.908 4.634
1324 asc-1 complex subunit p100. [refseq;acc:nm_032204]
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Divided 159.993 156.421 1.02284
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 216.542 211.908 4.634
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 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 218.509 213.648 1.02275
upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Subtracted 214.987 210.359 4.628
1327 eyes absent homolog 3. [swissprot;acc:q99504] 218.537 213.91 4.627
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Divided 218.509 213.648 1.02275
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 214.971 210.354 4.617
1329 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] 205.225 200.625 4.6
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Divided 218.509 213.648 1.02275
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 218.471 213.876 4.595
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 218.509 213.649 1.02275
1332 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Subtracted 218.471 213.876 4.595
cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Divided 220.681 215.78 1.02271
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 218.47 213.875 4.595
1334 jm4 protein. [refseq;acc:nm_007213] Divided 199.643 204.163 1.02264
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Subtracted 218.47 213.875 4.595
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 199.771 204.287 1.02261
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Subtracted 218.471 213.876 4.595
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 215.162 210.412 1.02257
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 218.47 213.875 4.595
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Divided 215.162 210.412 1.02257
1338 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Subtracted 218.47 213.875 4.595
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Divided 215.162 210.412 1.02257
1339 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Subtracted 218.471 213.876 4.595
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 205.204 200.71 1.02239
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] 226.433 231.491 1.02234

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/