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 1358 to 1407 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    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
    1391 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] PICALM
    1392 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] SNAP91 218.471 213.876
    1393 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] RC3H2 218.47 213.875
    1394 polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] PTBP1
    1395 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] GAS7 213.876
    1396 eyes absent homolog 1. [swissprot;acc:q99502] EYA1 218.463 213.872 1.02147
    1397 40s ribosomal protein s8. [swissprot;acc:p09058] RPS8 218.64 214.049 1.02145
    1398 eyes absent homolog 4. [swissprot;acc:o95677] EYA4 218.449 213.864 1.02144
    1399 eyes absent homolog 2. [swissprot;acc:o00167] EYA2 218.417 213.848 1.02137
    1400 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] ATF7 218.667 214.118 1.02125
    1401 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] ATF2 218.657 214.11 1.02124
    1402 colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] MCC 209.682 205.329 1.0212
    1403 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] ECHS1 184.656 180.823
    1404 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] SF3B4 232.752 237.65 1.02104
    1405 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] EIF3C 245.532 240.483 1.021
    1406 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] NR6A1 212.833 208.456
    1407 wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] WDFY1 206.104 210.424 1.02096

    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/