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 Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 912 to 961 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		network_comparison
    		green
    912 wd-repeat protein 3. [swissprot;acc:q9unx4] WDR3 243.896 1.03803 234.96
    913 prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] TGS1 210.863 1.03801 218.878
    914 pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] GOPC
    915 trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] TRMU 146.036 1.03798 140.692
    916 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] HAO2 232.512 1.03774 241.288
    917 parafibromin. [refseq;acc:nm_024529] CDC73 239.704 1.03772 230.991
    918 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] SORBS1 212.952 1.03731 205.292
    919 midasin (midas-containing protein). [swissprot;acc:q9nu22] MDN1 237.218 1.03725 228.698
    920 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] DEAF1 236.741 1.0372 245.547
    921 rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] RIOK1
    922 map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] MARK1
    923 map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] MARK2
    924 meiotic recombination protein spo11. [swissprot;acc:q9y5k1] SPO11
    925 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] PEF1 215.665 1.03714 207.942
    926 imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] IMMP2L 217.942 1.03713 210.139
    927 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] no value
    928 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] MTRF1 225.976 1.03651 218.017
    929 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] MPDU1 225.955 1.03642 218.015
    930 pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] PKM2 231.357 1.0364 239.778
    931 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] BHLHB4 159.13 1.03637 164.917
    932 mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] MTRF1L 225.939 1.03636 218.013
    933 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] BHLHB5 159.165 1.03635 164.951
    934 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] NOL6 242.024 1.03631 233.544
    935 sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] no value 232.473 1.03611 224.372
    936 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
    937 splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] SF3A3 220.246 1.03588 212.618
    938 splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] SF3A1
    939 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] BRCA1 216.501 224.27
    940 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] CAPNS1 212.442 1.03586 205.088
    941 swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] ARID1A 212.437 205.083
    942 grancalcin. [swissprot;acc:p28676] GCA 212.442 205.088
    943 sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] SRI 205.087
    944 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] PDCD6 212.437 205.083
    945 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] ARID1B 212.44 205.085
    946 histone h4. [swissprot;acc:p02304] no value 227.765 1.03576 219.902
    947 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] SORBS2 212.51 1.03567 205.191
    948 target of myb protein 1. [swissprot;acc:o60784] TOM1 217.254 1.03541 209.824
    949 huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] no value 217.253 1.0354 209.826
    950 dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] ERCC5 252.873 1.03539 261.821
    951 triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] TRIO 217.253 209.827
    952 target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] TOM1L2 217.252 1.03537 209.83
    953 polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] EXOSC10 198.494 1.03512 205.466
    954 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] GSTZ1 267.447 1.03487 276.773
    955 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] MRPL27 231.163 1.03479 239.205
    956 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] SORBS3 211.812 1.03458 204.732
    957 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF 129.913 1.03453 134.399
    958 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 129.921 1.03452 134.406
    959 guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] no value 237.558 1.03431 229.677
    960 zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] ZRF1
    961 serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] PPP2R5E 130.066 1.0343 134.527

    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/