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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2475 to 2524 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    310 Divided SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Measured 4909.79 5878.79 1.19736
    SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Ranked 242.153 266.673 1.10126
    Subtracted no value 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Measured 7551.8 8630.06 1078.26
    C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Squared 30651.3 38253.3 7602
    MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked 88.2482 110.265 22.0168
    TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Rooted 56.9506 64.7888 7.8382
    311 Divided 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] Squared 30566.4 38866.5 1.27154
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Measured 4981.52 5964.58 1.19734
    EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Ranked 242.627 267.151 1.10108
    MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Rooted 95.0526 85.3206 1.11406
    Subtracted no value 40s ribosomal protein s28. [swissprot;acc:p25112] Squared 30682.9 38183.6 7500.7
    APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Measured 2820.51 3897.1 1076.59
    MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Ranked 88.2482 110.265 22.0168
    RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Rooted 62.3337 70.0738 7.7401
    312 Divided no value methyltransferase like 2. [refseq;acc:nm_018396] Squared 71576.8 56326.7 1.27074
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Measured 4598.21 5500.48 1.19622
    MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Rooted 95.0526 85.3206 1.11406
    RPL3L 60s ribosomal protein l3-like. [swissprot;acc:q92901] Ranked 242.195 266.663 1.10103
    Subtracted no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 88.2482 110.265 22.0168
    DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Squared 33044.3 40524.8 7480.5
    MAX max protein. [swissprot;acc:p25912] Measured 4640.26 5704.87 1064.61
    NOSTRIN nostrin. [refseq;acc:nm_052946] Rooted 59.6399 51.9242 7.7157
    313 Divided DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Squared 71576.8 56326.7 1.27074
    MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted 95.0526 85.3206 1.11406
    PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Measured 21644.2 18098.7 1.1959
    RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Ranked 232.473 211.207 1.10069
    Subtracted FBLN2 fibulin-2 precursor. [swissprot;acc:p98095] Squared 45189.6 52666.2 7476.6
    LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Measured 4567.04 5631.2 1064.16
    MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked 88.2482 110.265 22.0168
    SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] Rooted 59.6399 51.9242 7.7157
    314 Divided FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared 71576.8 56326.7 1.27074
    METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Ranked 244.126 268.604 1.10027
    MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Rooted 95.0526 85.3206 1.11406
    PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Measured 21632.5 18090 1.19583
    Subtracted MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Ranked 88.2482 110.265 22.0168
    RNF25 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Squared 51519.3 44060.4 7458.9
    RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Measured 6563.65 7627.29 1063.64
    SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Rooted 59.6399 51.9242 7.7157
    315 Divided 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] Ranked 244.126 268.604 1.10027
    MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Rooted 95.0526 85.3206 1.11406
    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 56326.7 1.27074
    RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Measured 21370.8 17896.5 1.19413
    Subtracted GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Rooted 59.6399 51.9242 7.7157
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked 88.2482 110.265 22.0168
    RARS2 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Squared 31819.7 39222.2 7402.5
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] Measured 6644.99 7707.8 1062.81
    316 Divided no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Rooted 95.0526 85.3206 1.11406
    EIF1 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Ranked 242.694 267.017 1.10022
    PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Measured 21370.8 17896.5 1.19413
    WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Squared 28918.3 36746 1.27068

    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/