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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2508 to 2557 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    314 MYH3 Rooted myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Divided 95.0526 85.3206 1.11406
    PPP1R2P9 Measured type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 21632.5 18090 1.19583
    RNF25 Squared ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Subtracted 51519.3 44060.4 7458.9
    RRM2B Measured ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 6563.65 7627.29 1063.64
    SLC39A6 Rooted liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 59.6399 51.9242 7.7157
    315 GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
    MAGEC1 Ranked melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 88.2482 110.265 22.0168
    METAP2 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Divided 244.126 268.604 1.10027
    MYH1 Rooted myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 95.0526 85.3206 1.11406
    PCSK5 Squared proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] 71576.8 56326.7 1.27074
    RARS2 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Subtracted 31819.7 39222.2 7402.5
    RRS1 Measured ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Divided 21370.8 17896.5 1.19413
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] Subtracted 6644.99 7707.8 1062.81
    316 no value Rooted myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Divided 95.0526 85.3206 1.11406
    EIF1 Ranked protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 242.694 267.017 1.10022
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Subtracted 88.2482 110.265 22.0168
    NAPG Rooted gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 59.6399 51.9242 7.7157
    PPP1CA Measured serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Divided 21370.8 17896.5 1.19413
    RCC1 Squared regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Subtracted 44848.2 52108.3 7260.1
    WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Divided 28918.3 36746 1.27068
    WIPF1 Measured wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Subtracted 6603.41 7664.65 1061.24
    317 no value Ranked melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 88.2482 110.265 22.0168
    splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Divided 224.445 204.044 1.09998
    ADIPOR2 Measured adiponectin receptor 2. [refseq;acc:nm_024551] 3153.1 3762.56 1.19329
    GAD1 Rooted glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 59.6399 51.9242 7.7157
    MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Divided 95.0526 85.3206 1.11406
    NME3 Squared nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 33982.3 43159.1 1.27005
    VAV3 Measured vav-3 protein. [swissprot;acc:q9ukw4] Subtracted 6647.43 7706.18 1058.75
    ZEB2 Squared zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] 44848.2 52108.3 7260.1
    318 no value Measured nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided 34190.9 40795.8 1.19318
    AGPAT3 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Subtracted 7485.08 8543.66 1058.58
    CHRAC1 Rooted chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 38.8223 46.4975 7.6752
    MAGEA10 Ranked melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 88.2482 110.265 22.0168
    MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Divided 242.011 266.18 1.09987
    MYH13 Rooted myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 95.0526 85.3206 1.11406
    TOMM20 Squared mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 46739.9 59134.5 1.26518
    ZEB1 transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Subtracted 44848.2 52108.3 7260.1
    319 AGPAT4 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 7477 8532.02 1055.02
    B9D1 Rooted b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 53.4993 45.9227 7.5766
    MAGEB4 Ranked melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 88.2482 110.265 22.0168
    MPP3 Squared maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] 37147.5 44372.1 7224.6
    NIP7 Rooted saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Divided 49.0663 54.4978 1.1107
    PEX19 Squared peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 46739.9 59134.5 1.26518
    RPL19 Ranked 60s ribosomal protein l19. [swissprot;acc:p14118] 240.73 264.729 1.09969
    RRAGA Measured ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 20911 24908.5 1.19117
    320 no value Rooted 40s ribosomal protein s29. [swissprot;acc:p30054] 50.2784 45.294 1.11005
    CDH1 Ranked epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 241.892 265.96 1.0995
    COPA Squared coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Subtracted 49280.5 42272.7 7007.8
    CPA6 Rooted carboxypeptidase b precursor. [refseq;acc:nm_020361] 77.5801 70.0182 7.5619
    EPHX1 Squared epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Divided 87971.9 69563.1 1.26463

    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/