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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 8714 to 8763 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    2179 FABP3 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Subtracted High confidence 221.509 1.401 220.108
    KIRREL kin of irre like; nephrin related gene. [refseq;acc:nm_018240] Low confidence 201.026 3.749 197.277
    MTIF2 translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Divided 202.054 1.01904 198.279
    2180 no value brain protein 16. [refseq;acc:nm_016458] 188.304 1.01903 184.788
    HSPA8 heat shock cognate 71 kda protein. [swissprot;acc:p11142] High confidence 210.961 1.00667 209.563
    OPCML opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Subtracted Low confidence 201.95 3.749 198.201
    RPE65 retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] High confidence 221.509 1.401 220.108
    2181 no value tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Divided Low confidence 200.028 1.01903 196.292
    CALR calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] High confidence 227.117 1.00664 225.62
    INMT indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Subtracted 221.509 1.401 220.108
    KIRREL3 neph2. [refseq;acc:nm_032531] Low confidence 201.026 3.749 197.277
    2182 no value putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Divided 203.817 1.01903 200.011
    INMT indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Subtracted 201.016 3.749 197.267
    PEO1 twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] Divided High confidence 218.062 1.00664 216.624
    PXMP2 peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Subtracted 210.961 1.398 209.563
    2183 HSPA2 heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652]
    NDUFA6 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Low confidence 205.597 3.748 201.849
    PPP1CC serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Divided 198.177 1.01902 194.478
    RABEP1 rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] High confidence 218.062 1.00664 216.624
    2184 no value heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Subtracted 210.961 1.398 209.563
    GRPEL2 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Divided Low confidence 198.61 1.01902 194.903
    PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Subtracted 205.597 3.748 201.849
    SUPV3L1 suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Divided High confidence 211.713 1.00663 210.318
    2185 BAG1 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
    HSPA8 heat shock cognate 71 kda protein. [swissprot;acc:p11142] Subtracted 210.961 1.398 209.563
    SMOX polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Divided Low confidence 196.802 1.01902 193.129
    YWHAZ 14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] Subtracted 198.65 3.748 194.902
    2186 no value seven in absentia homolog 1. [refseq;acc:nm_003031] High confidence 223.608 1.397 225.005
    GSK3A glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Divided 211.713 1.00663 210.318
    GTF2A2 transcription initiation factor iia gamma chain (tfiia p12 subunit) (tfiia-12) (tfiias) (tfiia-gamma). [swissprot;acc:p52657] Low confidence 202.073 1.01901 198.303
    PNMT phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Subtracted 201.038 3.748 197.29
    2187 COPE coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] 201.692 197.944
    GSK3B glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Divided High confidence 211.713 1.00663 210.318
    LGALS4 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Subtracted 206.401 1.395 207.796
    WARS tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Divided Low confidence 199.859 1.01901 196.131
    2188 no value atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] 199.106 195.391
    P4HB protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] High confidence 209.54 1.00662 208.162
    PMS2 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Subtracted Low confidence 199.871 3.747 196.124
    SUPV3L1 suppressor of var1, 3-like 1. [refseq;acc:nm_003171] High confidence 211.713 1.395 210.318
    2189 BAG1 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
    DNA2L dna2-like homolog (dna replication helicase-like homolog) (fragment). [swissprot;acc:p51530] Low confidence 200.993 3.746 197.247
    HAAO 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Divided High confidence 209.54 1.00662 208.162
    KIRREL kin of irre like; nephrin related gene. [refseq;acc:nm_018240] Low confidence 201.026 1.019 197.277
    2190 CA10 carbonic anhydrase-related protein 10 (carbonic anhydrase-related protein x) (carp x) (ca-rp x) (cerebral protein-15) (hucep-15). [swissprot;acc:q9ns85] Subtracted 205.17 3.743 201.427
    GSK3A glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] High confidence 211.713 1.395 210.318
    SLC13A3 solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Divided Low confidence 194.356 1.019 190.732
    ZFPL1 zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] High confidence 209.54 1.00662 208.162
    2191 GSK3B glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Subtracted 211.713 1.395 210.318
    HUS1 hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] Divided 209.54 1.00662 208.162
    KIRREL3 neph2. [refseq;acc:nm_032531] Low confidence 201.026 1.019 197.277

    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/