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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 Gene description Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1341 to 1390 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    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 226.433 231.491 1.02234
    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
    1380 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] USP8 213.876
    1381 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] ROD1
    1382 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] PTBP2
    1383 adaptor-associated kinase 1. [refseq;acc:nm_014911] AAK1
    1384 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] ATN1 218.471
    1385 dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] no value 218.47 213.875
    1386 rho-gtpase activating protein 10. [refseq;acc:nm_020824] ARHGAP21 213.876
    1387 sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] SALL1 213.875
    1388 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] SALL4 218.471 213.876
    1389 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] BCKDHB 218.47 213.875
    1390 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] CNOT4

    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/