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 description Gene Value Type Network Comparison Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 2680 to 2729 of 6456 in total
Value Type	Ranked
Interaction Map High confidence
Filtered 1
Rank description Network Comparison Type red network_comparison green 1340 membrane-associated nucleic acid binding protein. [source:refseq;acc:nm_018835] Subtracted 218.47 4.595 213.875 1341 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [source:swissprot;acc:p05198] Divided 226.433 1.02234 231.491 1341 polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [source:swissprot;acc:p26599] Subtracted 218.47 4.595 213.875 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). [source:swissprot;acc:o43463] Divided 226.433 1.02234 231.491 1342 sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9] Subtracted 218.47 4.594 213.876 1343 m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [source:swissprot;acc:p30304] Divided 258.558 1.02231 252.916 1343 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [source:swissprot;acc:p40818] Subtracted 218.47 4.594 213.876 1344 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [source:refseq;acc:nm_006027] Divided 216.772 1.02224 221.594 1344 rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [source:refseq;acc:nm_005156] Subtracted 218.47 4.594 213.876 1345 phd finger protein 9. [source:refseq;acc:nm_018062] Divided 216.772 1.02224 221.594 1345 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [source:refseq;acc:nm_021190] Subtracted 218.47 4.594 213.876 1346 adaptor-associated kinase 1. [source:refseq;acc:nm_014911] Subtracted 218.47 4.594 213.876 1346 small optic lobes homolog; small optic lobes, drosophila, homolog of. [source:refseq;acc:nm_005632] Divided 216.772 1.02224 221.594 1347 lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [source:swissprot;acc:o43766] Divided 204.961 1.02223 209.517 1347 rho-gtpase activating protein 10. [source:refseq;acc:nm_020824] Subtracted 218.47 4.594 213.876 1348 growth-arrest-specific protein 7 (gas-7). [source:swissprot;acc:o60861] Subtracted 218.47 4.594 213.876 1348 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915] Divided 218.569 1.02215 213.832 1349 40s ribosomal protein s8. [source:swissprot;acc:p09058] Subtracted 218.64 4.591 214.049 1349 zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481] Divided 218.572 1.02212 213.841 1350 eyes absent homolog 1. [source:swissprot;acc:q99502] Subtracted 218.463 4.591 213.872 1350 zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [source:swissprot;acc:o95409] Divided 218.574 1.0221 213.847 1351 eyes absent homolog 4. [source:swissprot;acc:o95677] Subtracted 218.449 4.585 213.864 1351 prohibitin. [source:swissprot;acc:p35232] Divided 211.513 1.02209 206.941 1352 prohibitin. [source:swissprot;acc:p35232] Subtracted 211.513 4.572 206.941 1352 repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273] Divided 211.513 1.02209 206.941 1353 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [source:swissprot;acc:p52849] Divided 228.409 1.02208 223.475 1353 repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273] Subtracted 211.513 4.572 206.941 1354 eyes absent homolog 2. [source:swissprot;acc:o00167] Subtracted 218.417 4.569 213.848 1354 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [source:refseq;acc:nm_004784] Divided 228.409 1.02208 223.475 1355 lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [source:swissprot;acc:o43766] Subtracted 204.961 4.556 209.517 1355 n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569] Divided 228.409 1.02208 223.475 1356 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [source:swissprot;acc:p17544] Subtracted 218.667 4.549 214.118 1356 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). [source:swissprot;acc:p52848] Divided 228.409 1.02208 223.475 1357 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [source:swissprot;acc:p15336] Subtracted 218.657 4.547 214.11 1357 protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260] Divided 228.409 1.02208 223.475 1358 geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [source:swissprot;acc:p53609] Subtracted 225.039 4.534 229.573 1358 upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415] Divided 214.987 1.022 210.359 1359 fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [source:refseq;acc:nm_021727] Subtracted 225.039 4.534 229.573 1359 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712] Divided 228.642 1.02197 223.726 1360 mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [source:swissprot;acc:q13485] Subtracted 225.039 4.534 229.573 1360 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). [source:swissprot;acc:p36897] Divided 223.89 1.02195 228.805 1361 fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [source:refseq;acc:nm_004265] Subtracted 225.039 4.534 229.573 1361 upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [source:swissprot;acc:q15853] Divided 214.971 1.02195 210.354 1362 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402] Subtracted 225.039 4.534 229.573 1362 peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911] Divided 228.644 1.02194 223.736 1363 camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904] Divided 218.591 1.02194 213.899 1363 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4] Subtracted 168.989 4.529 164.46 1364 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5] Subtracted 168.995 4.528 164.467 1364 serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [source:swissprot;acc:p36896] Divided 223.885 1.02194 228.797 1365 atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2] Divided 228.644 1.02194 223.736 Legend: - Rank is the rank after comparing the two networks - 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/