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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map red Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 1125 to 1174 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 165 GAD2 209.299 1.19058 249.187
    glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 167 GAD1
    glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] 1444 GLUDP5 203.908 1.02006 207.998
    glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 1443 GLUD2
    glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] 1229 GCLC 213.079 1.02462 218.325
    glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] 1228 GCLM
    glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 2674 GLUL 203.151 1.001 202.948
    glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 1217 QRSL1 211.959 1.025 217.258
    glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 1470 QARS 221.412 1.0194 217.199
    glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075] 2957 ENPEP 0.00001 1 0.00001
    glutamyl trna synthetase. [sptrembl;acc:o14563] 1473 EARS2 221.412 1.0194 217.199
    glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] 2167 GCDH 215.925 1.00673 214.481
    glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] 1304 GSR 207.387 1.02357 212.275
    glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] 1677 GSTP1 218.654 1.01408 221.732
    glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 1371 GSTT1 228.646 1.02191 223.744
    glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 1359 GSTT2B 228.642 1.02197 223.726
    glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 239 GSTO1 227.357 1.11785 254.15
    glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] 2348 GAPDH 217.057 1.00448 218.03
    glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 2549 no value 206.902 1.00185 206.519
    glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] 2548 206.899 206.516
    glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 2547 206.894 1.00186 206.51
    glycerol-3-phosphate acyltransferase, mitochondrial precursor (ec 2.3.1.15) (gpat). [swissprot;acc:q9hcl2] 3033 GPAM 0.00001 1 0.00001
    glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 2669 GPD1 214.575 1.00103 214.354
    glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] 2534 GPD2 208 1.00214 207.555
    glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] 1296 SLC37A1 209.062 1.02394 204.174
    glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 2343 no value 212.222 1.00451 211.27
    glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 2448 212.446 1.00321 211.766
    glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [swissprot;acc:p23415] 2919 GLRA1 0.00001 1 0.00001
    glycine receptor alpha-2 chain precursor. [swissprot;acc:p23416] 3121 GLRA2
    glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] 2920 GLRA3
    glycine receptor beta chain precursor (glycine receptor 58 kda subunit). [swissprot;acc:p48167] 3083 GLRB
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 19 PYGB 185.678 1.32082 245.247
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 20 PYGL
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 22 PYGM
    glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] 2186 GSK3A 211.713 1.00663 210.318
    glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] 2187 GSK3B
    glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 1324 GYS2 159.993 1.02284 156.421
    glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 1319 GYS1 159.75 1.02304 156.153
    glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] 2562 GYG1 208.429 1.00168 208.779
    glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] 2565 GYG2
    glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] 1472 GARS 221.412 1.0194 217.199
    gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] 1694 GMPS 218.937 1.01373 215.971
    golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] 1177 ACBD3 218.186 1.02593 212.672
    golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] 1960 YIPF5 211.633 1.00978 213.703
    golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 1835 GORASP2 194.573 1.01132 192.396
    goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] 1994 COL4A3BP 189.011 1.0094 190.787
    gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [swissprot;acc:q96s52] 3165 PIGS 0.00001 1 0.00001
    grancalcin. [swissprot;acc:p28676] 942 GCA 212.442 1.03586 205.088
    grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] 551 GRAP2 207.261 1.06645 194.347
    grb2-related adaptor protein. [swissprot;acc:q13588] 441 GRAP 223.457 1.07835 207.222

    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/