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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2675 to 2724 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1338 GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Divided 215.162 210.412 1.02257
PICALM phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Subtracted 218.47 213.875 4.595
1339 NPC2 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
SNAP91 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
1340 RC3H2 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] 218.47 213.875
SUV39H2 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] Divided 226.433 231.491 1.02234
1341 EIF2S1 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198]
PTBP1 polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Subtracted 218.47 213.875 4.595
1342 SALL3 sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] 213.876 4.594
SUV39H1 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 226.433 231.491 1.02234
1343 CDC25A m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] 258.558 252.916 1.02231
USP8 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 218.47 213.876 4.594
1344 EXO1 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Divided 216.772 221.594 1.02224
ROD1 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 218.47 213.876 4.594
1345 FANCL phd finger protein 9. [refseq;acc:nm_018062] Divided 216.772 221.594 1.02224
PTBP2 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Subtracted 218.47 213.876 4.594
1346 AAK1 adaptor-associated kinase 1. [refseq;acc:nm_014911]
SOLH small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] Divided 216.772 221.594 1.02224
1347 ARHGAP21 rho-gtpase activating protein 10. [refseq;acc:nm_020824] Subtracted 218.47 213.876 4.594
LIAS lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] Divided 204.961 209.517 1.02223
1348 GAS7 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] Subtracted 218.47 213.876 4.594
ZIC1 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Divided 218.569 213.832 1.02215
1349 RPS8 40s ribosomal protein s8. [swissprot;acc:p09058] Subtracted 218.64 214.049 4.591
ZIC3 zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Divided 218.572 213.841 1.02212
1350 EYA1 eyes absent homolog 1. [swissprot;acc:q99502] Subtracted 218.463 213.872 4.591
ZIC2 zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Divided 218.574 213.847 1.0221
1351 EYA4 eyes absent homolog 4. [swissprot;acc:o95677] Subtracted 218.449 213.864 4.585
PHB prohibitin. [swissprot;acc:p35232] Divided 211.513 206.941 1.02209
1352 no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]
PHB prohibitin. [swissprot;acc:p35232] Subtracted 4.572
1353 no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]
NDST2 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Divided 228.409 223.475 1.02208
1354 EYA2 eyes absent homolog 2. [swissprot;acc:o00167] Subtracted 218.417 213.848 4.569
NDST3 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Divided 228.409 223.475 1.02208
1355 LIAS lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] Subtracted 204.961 209.517 4.556
NDST4 n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Divided 228.409 223.475 1.02208
1356 ATF7 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Subtracted 218.667 214.118 4.549
NDST1 heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] Divided 228.409 223.475 1.02208
1357 ATF2 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Subtracted 218.657 214.11 4.547
CDC27 protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Divided 228.409 223.475 1.02208
1358 PGGT1B geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] Subtracted 225.039 229.573 4.534
USF1 upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Divided 214.987 210.359 1.022
1359 FADS3 fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] Subtracted 225.039 229.573 4.534
GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Divided 228.642 223.726 1.02197
1360 SMAD4 mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] Subtracted 225.039 229.573 4.534
TGFBR1 tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] Divided 223.89 228.805 1.02195
1361 FADS2 fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265] Subtracted 225.039 229.573 4.534
USF2 upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Divided 214.971 210.354 1.02195
1362 no value fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Subtracted 225.039 229.573 4.534
PAOX peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Divided 228.644 223.736 1.02194

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/