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 Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2501 to 2550 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    313 MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted Divided 95.0526 1.11406 85.3206
    PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Measured 21644.2 1.1959 18098.7
    RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Ranked 232.473 1.10069 211.207
    SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] Rooted Subtracted 59.6399 7.7157 51.9242
    314 FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared Divided 71576.8 1.27074 56326.7
    MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Ranked Subtracted 88.2482 22.0168 110.265
    METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Divided 244.126 1.10027 268.604
    MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Rooted 95.0526 1.11406 85.3206
    PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Measured 21632.5 1.19583 18090
    RNF25 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Squared Subtracted 51519.3 7458.9 44060.4
    RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Measured 6563.65 1063.64 7627.29
    SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Rooted 59.6399 7.7157 51.9242
    315 GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked 88.2482 22.0168 110.265
    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 1.10027 268.604
    MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Rooted 95.0526 1.11406 85.3206
    PCSK5 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] Squared 71576.8 1.27074 56326.7
    RARS2 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Subtracted 31819.7 7402.5 39222.2
    RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Measured Divided 21370.8 1.19413 17896.5
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] Subtracted 6644.99 1062.81 7707.8
    316 no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Rooted Divided 95.0526 1.11406 85.3206
    EIF1 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Ranked 242.694 1.10022 267.017
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Subtracted 88.2482 22.0168 110.265
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Rooted 59.6399 7.7157 51.9242
    PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Measured Divided 21370.8 1.19413 17896.5
    RCC1 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Squared Subtracted 44848.2 7260.1 52108.3
    WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Divided 28918.3 1.27068 36746
    WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Measured Subtracted 6603.41 1061.24 7664.65
    317 no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Ranked 88.2482 22.0168 110.265
    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 1.09998 204.044
    ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Measured 3153.1 1.19329 3762.56
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Rooted Subtracted 59.6399 7.7157 51.9242
    MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Divided 95.0526 1.11406 85.3206
    NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Squared 33982.3 1.27005 43159.1
    VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Measured Subtracted 6647.43 1058.75 7706.18
    ZEB2 zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Squared 44848.2 7260.1 52108.3
    318 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Measured Divided 34190.9 1.19318 40795.8
    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 1058.58 8543.66
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Rooted 38.8223 7.6752 46.4975
    MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked 88.2482 22.0168 110.265
    MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Divided 242.011 1.09987 266.18
    MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Rooted 95.0526 1.11406 85.3206
    TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Squared 46739.9 1.26518 59134.5
    ZEB1 transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Subtracted 44848.2 7260.1 52108.3
    319 AGPAT4 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] Measured 7477 1055.02 8532.02
    B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Rooted 53.4993 7.5766 45.9227
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Ranked 88.2482 22.0168 110.265
    MPP3 maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Squared 37147.5 7224.6 44372.1
    NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Rooted Divided 49.0663 1.1107 54.4978
    PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Squared 46739.9 1.26518 59134.5

    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/