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 Gene Rank Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1075 to 1124 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] 884 no value 227.596 219.017 1.03917
    gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 48 GABARAP 65.4586 83.0461 1.26868
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 168 no value 82.5916 98.0548 1.18722
    galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] 1337 215.162 210.412 1.02257
    galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 2158 LGALS4 206.401 207.796 1.00676
    galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] 2122 LGALS9 206.473 207.911 1.00696
    gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 1934 ADD3 224.264 222.055 1.00995
    gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] 2360 ENO2 207.186 208.046 1.00415
    gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 628 GABRA1 214.256 202.14 1.05994
    gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 621 GABRA2
    gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 629 GABRA3
    gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 625 GABRA4
    gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 622 GABRA6
    gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 626 GABRE
    gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 620 GABRG1
    gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 623 GABRG2
    gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 618 GABRG3 202.139
    gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] 1842 BBOX1 212.455 210.113 1.01115
    gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284] 3101 no value 0.00001 0.00001 1
    gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] 1181 SGCG 218.186 212.672 1.02593
    gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] 1817 RAB11FIP5 220.462 217.926 1.01164
    gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 166 NAPG 209.299 249.187 1.19058
    ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 1139 GDAP1L1 218.484 212.675 1.02731
    ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 1141 GDAP1
    gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] 2470 PGC 235.812 235.088 1.00308
    gbp protein isoform a. [refseq;acc:nm_017870] 47 TMEM132A 325.586 256.492 1.26938
    gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] 2539 C21orf66 217.144 216.699 1.00205
    gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] 979 BLOC1S1 202.027 195.386 1.03399
    gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488] 3125 POFUT1 0.00001 0.00001 1
    gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] 1894 GMPPA 222.842 225.17 1.01045
    gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 1893 GMPPB
    general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] 2732 GCN5L2 202.233 202.175 1.00029
    general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] 1923 USO1 220.659 218.452 1.0101
    geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] 2536 GGPS1 236.51 236.008 1.00213
    geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] 1438 PGGT1B 225.039 229.573 1.02015
    geranylgeranyl transferase type ii beta subunit (ec 2.5.1.-) (rab geranylgeranyltransferase beta subunit) (rab geranyl- geranyltransferase beta subunit) (rab gg transferase beta) (rab ggtase beta). [swissprot;acc:p53611] 2963 RABGGTB 0.00001 0.00001 1
    germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] 2685 YBX2 208.438 208.635 1.00095
    germ cell-less. [refseq;acc:nm_022471] 1780 no value 206.335 203.877 1.01206
    gk001 protein. [refseq;acc:nm_020198] 2704 CCDC47 188.435 188.311 1.00066
    glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] 1373 GMFG 216.542 211.908 1.02187
    glioma pathogenesis-related protein (glipr) (rtvp-1 protein). [swissprot;acc:p48060] 2953 GLIPR1 0.00001 0.00001 1
    glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] 3104 SNORD23
    glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] 3007 YEATS4
    glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 2084 no value 222.548 224.293 1.00784
    glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] 2090 GFPT2 222.609 224.344 1.00779
    glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 3058 GNPDA1 0.00001 0.00001 1
    glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] 2861 GNPDA2
    glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] 1701 G6PD 216.079 219.024 1.01363
    glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] 1491 GPI 217.704 221.839 1.01899
    glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] 2365 CNDP1 208.958 209.82 1.00413

    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/