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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1330 to 1379 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
1330 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] RCAN1 218.508 213.648 1.02275
1331 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] RCAN3 218.509 213.649
1332 cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] OXA1L 220.681 215.78 1.02271
1333 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] MRPL34
1334 jm4 protein. [refseq;acc:nm_007213] PRAF2 199.643 204.163 1.02264
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] ARL6IP5 199.771 204.287 1.02261
1336 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] GALK2 215.162 210.412 1.02257
1337 galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] no value
1338 udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] GALE
1339 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] NPC2 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] SUV39H2 226.433 231.491 1.02234
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] EIF2S1
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] SUV39H1
1343 m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] CDC25A 258.558 252.916 1.02231
1344 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] EXO1 216.772 221.594 1.02224
1345 phd finger protein 9. [refseq;acc:nm_018062] FANCL
1346 small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] SOLH
1347 lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] LIAS 204.961 209.517 1.02223
1348 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] ZIC1 218.569 213.832 1.02215
1349 zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] ZIC3 218.572 213.841 1.02212
1350 zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] ZIC2 218.574 213.847 1.0221
1351 prohibitin. [swissprot;acc:p35232] PHB 211.513 206.941 1.02209
1352 repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] no value
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] NDST2 228.409 223.475 1.02208
1354 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] NDST3
1355 n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] NDST4
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). [swissprot;acc:p52848] NDST1
1357 protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] CDC27
1358 upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] USF1 214.987 210.359 1.022
1359 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] GSTT2B 228.642 223.726 1.02197
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). [swissprot;acc:p36897] TGFBR1 223.89 228.805 1.02195
1361 upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] USF2 214.971 210.354
1362 peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] PAOX 228.644 223.736 1.02194
1363 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] CREB5 218.591 213.899
1364 serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] ACVR1B 223.885 228.797
1365 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] ATPIF1 228.644 223.736
1366 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] ACVR1C 223.884 228.795
1367 neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] FREQ 223.887 228.799
1368 polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] SMOX 228.644 223.736
1369 cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] HCCS
1370 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] NCK1 205.185 200.784 1.02192
1371 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] GSTT1 228.646 223.744 1.02191
1372 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] SOCS1 216.542 211.908 1.02187
1373 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] GMFG
1374 asc-1 complex subunit p100. [refseq;acc:nm_032204] ASCC2
1375 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] FKBP1A
1376 eyes absent homolog 3. [swissprot;acc:q99504] EYA3 218.537 213.91 1.02163
1377 sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] SALL2 218.471 213.876 1.02148
1378 sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] SALL3 218.47
1379 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] RERE 213.875

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/