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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1358 to 1407 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		network_comparison
    		green
    1358 USF1 upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] 214.987 1.022 210.359
    1359 GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 228.642 1.02197 223.726
    1360 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] 223.89 1.02195 228.805
    1361 USF2 upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] 214.971 210.354
    1362 PAOX peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 228.644 1.02194 223.736
    1363 CREB5 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 218.591 213.899
    1364 ACVR1B 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] 223.885 228.797
    1365 ATPIF1 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] 228.644 223.736
    1366 ACVR1C activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] 223.884 228.795
    1367 FREQ neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] 223.887 228.799
    1368 SMOX polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] 228.644 223.736
    1369 HCCS cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]
    1370 NCK1 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] 205.185 1.02192 200.784
    1371 GSTT1 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 228.646 1.02191 223.744
    1372 SOCS1 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] 216.542 1.02187 211.908
    1373 GMFG glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
    1374 ASCC2 asc-1 complex subunit p100. [refseq;acc:nm_032204]
    1375 FKBP1A 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]
    1376 EYA3 eyes absent homolog 3. [swissprot;acc:q99504] 218.537 1.02163 213.91
    1377 SALL2 sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] 218.471 1.02148 213.876
    1378 SALL3 sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] 218.47
    1379 RERE arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 213.875
    1380 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] 213.876
    1381 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]
    1382 PTBP2 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]
    1383 AAK1 adaptor-associated kinase 1. [refseq;acc:nm_014911]
    1384 ATN1 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] 218.471
    1385 no value dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 218.47 213.875
    1386 ARHGAP21 rho-gtpase activating protein 10. [refseq;acc:nm_020824] 213.876
    1387 SALL1 sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] 213.875
    1388 SALL4 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 218.471 213.876
    1389 BCKDHB 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] 218.47 213.875
    1390 CNOT4 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316]
    1391 PICALM phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492]
    1392 SNAP91 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] 218.471 213.876
    1393 RC3H2 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] 218.47 213.875
    1394 PTBP1 polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]
    1395 GAS7 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] 213.876
    1396 EYA1 eyes absent homolog 1. [swissprot;acc:q99502] 218.463 1.02147 213.872
    1397 RPS8 40s ribosomal protein s8. [swissprot;acc:p09058] 218.64 1.02145 214.049
    1398 EYA4 eyes absent homolog 4. [swissprot;acc:o95677] 218.449 1.02144 213.864
    1399 EYA2 eyes absent homolog 2. [swissprot;acc:o00167] 218.417 1.02137 213.848
    1400 ATF7 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 218.667 1.02125 214.118
    1401 ATF2 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 218.657 1.02124 214.11
    1402 MCC colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] 209.682 1.0212 205.329
    1403 ECHS1 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 184.656 180.823
    1404 SF3B4 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] 232.752 1.02104 237.65
    1405 EIF3C eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 245.532 1.021 240.483
    1406 NR6A1 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] 212.833 208.456
    1407 WDFY1 wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] 206.104 1.02096 210.424

    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/