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 Interaction Map Network Comparison Type Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2551 to 2600 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    1276 CHRNA3 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Divided 171.231 167.177 1.02425
    PPP3CB serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] Subtracted 218.44 213.44 5
    1277 POLE3 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 250.854 255.842 4.988
    SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Divided 171.231 167.177 1.02425
    1278 NDST2 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Subtracted 228.409 223.475 4.934
    SESN3 sestrin 3. [swissprot;acc:p58005] Divided 218.368 213.219 1.02415
    1279 NDST3 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Subtracted 228.409 223.475 4.934
    SESN2 sestrin 2 (hi95). [swissprot;acc:p58004] Divided 218.368 213.219 1.02415
    1280 CYP4A11 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 213.22 1.02414
    NDST4 n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Subtracted 228.409 223.475 4.934
    1281 CYP4F3 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Divided 218.368 213.22 1.02414
    NDST1 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] Subtracted 228.409 223.475 4.934
    1282 CDC27 protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260]
    CYP4F8 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Divided 218.368 213.22 1.02414
    1283 CYP4X1 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]
    DLAT 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] Subtracted 206.482 211.404 4.922
    1284 CYP4F12 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Divided 218.368 213.22 1.02414
    GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Subtracted 228.642 223.726 4.916
    1285 CYP4F2 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Divided 218.368 213.22 1.02414
    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] Subtracted 223.89 228.805 4.915
    1286 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 4.912
    CYP4F11 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Divided 218.368 213.22 1.02414
    1287 CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]
    FREQ neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Subtracted 223.887 228.799 4.912
    1288 ACVR1C activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] 223.884 228.795 4.911
    CYP4B1 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Divided 218.368 213.22 1.02414
    1289 FLOT1 flotillin-1. [swissprot;acc:o75955]
    PAOX peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Subtracted 228.644 223.736 4.908
    1290 ATPIF1 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]
    SESN1 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] Divided 218.368 213.22 1.02414
    1291 HAS2 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] 221.093 226.399 1.024
    SMOX polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Subtracted 228.644 223.736 4.908
    1292 CASP7 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Divided 233.942 228.46 1.024
    HCCS cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Subtracted 228.644 223.736 4.908
    1293 CASP3 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] Divided 233.942 228.46 1.024
    TPD52L2 tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] Subtracted 206.852 211.757 4.905
    1294 GSTT1 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 228.646 223.744 4.902
    HAS1 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Divided 221.093 226.399 1.024
    1295 HAS3 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219]
    OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Subtracted 220.681 215.78 4.901
    1296 MRPL34 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]
    SLC37A1 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Divided 209.062 204.174 1.02394
    1297 PRODH proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272]
    SF3B4 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Subtracted 232.752 237.65 4.898
    1298 DLAT 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] Divided 206.482 211.404 1.02384
    SLC37A1 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Subtracted 209.062 204.174 4.888
    1299 GSR glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] 207.387 212.275
    PMPCB mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Divided 217.635 212.575 1.0238
    1300 PMPCA mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 217.634 212.576 1.02379
    PRODH proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Subtracted 209.062 204.174 4.888

    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/