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 green network_comparison
    Results: HTML CSV LaTeX Showing element 891 to 940 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    891 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] DIRAS1 212.028 204.055 1.03907
    892 di-ras2. [refseq;acc:nm_017594] DIRAS2
    893 myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] MYC 227.585 219.037 1.03903
    894 phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] FARSA 217.491 209.323 1.03902
    895 phenylalanine-trna synthetase. [refseq;acc:nm_006567] FARS2
    896 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] POLR2J 230.811 239.785 1.03888
    897 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] PDPK1 272.878 283.472 1.03882
    898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] no value 229.171 238.048 1.03874
    899 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] TXNDC2
    900 thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] TXN
    901 structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] SSRP1 237.62 228.762 1.03872
    902 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] SUPT16H
    903 eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] EIF3G 246.354 237.223 1.03849
    904 eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] EIF3A
    905 dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] no value 230.768 239.632 1.03841
    906 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 230.764 239.62 1.03838
    907 junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] JUP 223.906 215.653 1.03827
    908 tax interaction protein 1. [refseq;acc:nm_014604] no value
    909 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] SEPT1 142.077 136.846 1.03823
    910 uba/ubx 33.3 kda protein. [swissprot;acc:q04323] no value 217.168 209.207 1.03805
    911 ero1-like. [refseq;acc:nm_014584]
    912 wd-repeat protein 3. [swissprot;acc:q9unx4] WDR3 243.896 234.96 1.03803
    913 prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] TGS1 210.863 218.878 1.03801
    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 146.036 140.692 1.03798
    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 232.512 241.288 1.03774
    917 parafibromin. [refseq;acc:nm_024529] CDC73 239.704 230.991 1.03772
    918 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] SORBS1 212.952 205.292 1.03731
    919 midasin (midas-containing protein). [swissprot;acc:q9nu22] MDN1 237.218 228.698 1.03725
    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 236.741 245.547 1.0372
    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 215.665 207.942 1.03714
    926 imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] IMMP2L 217.942 210.139 1.03713
    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 225.976 218.017 1.03651
    929 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] MPDU1 225.955 218.015 1.03642
    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 231.357 239.778 1.0364
    931 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] BHLHB4 159.13 164.917 1.03637
    932 mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] MTRF1L 225.939 218.013 1.03636
    933 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] BHLHB5 159.165 164.951 1.03635
    934 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] NOL6 242.024 233.544 1.03631
    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 232.473 224.372 1.03611
    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 220.246 212.618 1.03588
    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 212.442 205.088 1.03586

    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/