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 Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2675 to 2724 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1338 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] Low confidence 204.159 199.739 1.02213
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] High confidence 215.162 210.412 1.02257
1339 choline/ethanolaminephosphotransferase. [refseq;acc:nm_006090] Low confidence 187.632 183.57 1.02213
epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] High confidence 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
tbc1 domain family member 5. [swissprot;acc:q92609] Low confidence 203.872 199.458 1.02213
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] High confidence 226.433 231.491 1.02234
reversion-inducing cysteine-rich protein with kazal motifs precursor (hreck) (suppressor of tumorigenicity 15) (st15). [swissprot;acc:o95980] Low confidence 187.632 183.57 1.02213
1342 choline phosphotransferase 1; cholinephosphotransferase 1 alpha; cholinephosphotransferase 1. [refseq;acc:nm_020244] 187.631 183.569
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] High confidence 226.433 231.491 1.02234
1343 m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] 258.558 252.916 1.02231
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Low confidence 153.029 156.416 1.02213
1344 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 204.058 199.639
exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] High confidence 216.772 221.594 1.02224
1345 esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Low confidence 200.431 196.093 1.02212
phd finger protein 9. [refseq;acc:nm_018062] High confidence 216.772 221.594 1.02224
1346 small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Low confidence 201.165 196.812 1.02212
1347 lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] High confidence 204.961 209.517 1.02223
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Low confidence 205.323 200.881 1.02211
1348 peptidyl-prolyl cis-trans isomerase, mitochondrial precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin f). [swissprot;acc:p30405] 201.458 197.1
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] High confidence 218.569 213.832 1.02215
1349 carboxypeptidase a5. [refseq;acc:nm_080385] Low confidence 187.671 183.613 1.0221
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] High confidence 218.572 213.841 1.02212
1350 t-complex protein 1, theta subunit (tcp-1-theta) (cct-theta). [swissprot;acc:p50990] Low confidence 201.762 197.399 1.0221
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] High confidence 218.574 213.847
1351 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Low confidence 211.431 216.104
prohibitin. [swissprot;acc:p35232] High confidence 211.513 206.941 1.02209
1352 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Low confidence 187.651 183.595
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] High confidence 211.513 206.941
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] 228.409 223.475 1.02208
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Low confidence 201.009 196.664 1.02209
1354 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] High confidence 228.409 223.475 1.02208
ubiquilin 1 isoform 1. [refseq;acc:nm_013438] Low confidence 206.622 202.158
1355 n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] High confidence 228.409 223.475
ras gtpase-activating protein 3 (gap1(ip4bp)) (ins p4-binding protein). [swissprot;acc:q14644] Low confidence 202.643 198.269 1.02206
1356 ca2+-promoted ras inactivator; gtpase activating protein-like; calcium-promoted ras inactivator. [refseq;acc:nm_006989]
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] High confidence 228.409 223.475 1.02208
1357 protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260]
ras gtpase-activating protein 2 (gap1m). [swissprot;acc:q15283] Low confidence 202.643 198.269 1.02206
1358 rasgap-activating-like protein 1. [swissprot;acc:o95294]
upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] High confidence 214.987 210.359 1.022
1359 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 228.642 223.726 1.02197
rasgap-activating-like protein 2. [swissprot;acc:o43374] Low confidence 202.643 198.269 1.02206
1360 peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 201.201 196.865 1.02203
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] High confidence 223.89 228.805 1.02195
1361 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Low confidence 203.394 199.014 1.02201
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] High confidence 214.971 210.354 1.02195
1362 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] Low confidence 203.714 199.329 1.022
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] High confidence 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
- 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/