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 Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
1329 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Divided 213.648 218.509 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 213.876 218.471 4.595
1331 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 213.875 218.47
calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] Divided 213.649 218.509 1.02275
1332 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Subtracted 213.876 218.471 4.595
cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Divided 215.78 220.681 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 213.875 218.47 4.595
1334 jm4 protein. [refseq;acc:nm_007213] Divided 204.163 199.643 1.02264
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Subtracted 213.875 218.47 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 204.287 199.771 1.02261
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Subtracted 213.876 218.471 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] 213.875 218.47
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Divided 210.412 215.162 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 213.875 218.47 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 210.412 215.162 1.02257
1338 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Subtracted 213.875 218.47 4.595
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Divided 210.412 215.162 1.02257
1339 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Subtracted 213.876 218.471 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 200.71 205.204 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] 231.491 226.433 1.02234
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Subtracted 213.875 218.47 4.595
1341 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] Divided 231.491 226.433 1.02234
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Subtracted 213.875 218.47 4.595
1342 histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] Divided 231.491 226.433 1.02234
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Subtracted 213.876 218.47 4.594
1343 m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Divided 252.916 258.558 1.02231
ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Subtracted 213.876 218.47 4.594
1344 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Divided 221.594 216.772 1.02224
rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] Subtracted 213.876 218.47 4.594
1345 phd finger protein 9. [refseq;acc:nm_018062] Divided 221.594 216.772 1.02224
polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Subtracted 213.876 218.47 4.594
1346 adaptor-associated kinase 1. [refseq;acc:nm_014911]
small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] Divided 221.594 216.772 1.02224
1347 lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] 209.517 204.961 1.02223
rho-gtpase activating protein 10. [refseq;acc:nm_020824] Subtracted 213.876 218.47 4.594
1348 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861]
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Divided 213.832 218.569 1.02215
1349 40s ribosomal protein s8. [swissprot;acc:p09058] Subtracted 214.049 218.64 4.591
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Divided 213.841 218.572 1.02212
1350 eyes absent homolog 1. [swissprot;acc:q99502] Subtracted 213.872 218.463 4.591
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Divided 213.847 218.574 1.0221
1351 eyes absent homolog 4. [swissprot;acc:o95677] Subtracted 213.864 218.449 4.585
prohibitin. [swissprot;acc:p35232] Divided 206.941 211.513 1.02209
1352 Subtracted 4.572
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Divided 1.02209
1353 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] 223.475 228.409 1.02208
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Subtracted 206.941 211.513 4.572
1354 eyes absent homolog 2. [swissprot;acc:o00167] 213.848 218.417 4.569

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/