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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2401 to 2450 of 14920 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    		description
    		Value Type
    		Filtered
    		red
    		green
    		network_comparison
    301 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Ranked 1 150.982 166.372 1.10193
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Measured 13768.2 11466 1.20078
    dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Rooted 0 12.7534 11.8854 1.07303
    forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Measured 135.294 149.371 1.10405
    kappa b-ras 1. [refseq;acc:nm_020345] Squared 1558.15 1297.17 1.20119
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Rooted 1 203.673 182.638 1.11517
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared 28896.2 36767 1.27238
    sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] Ranked 0 12783 13698 1.07158
    302 60s ribosomal protein l26. [swissprot;acc:q02877] 1 242.326 267.008 1.10185
    cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Squared 0 61.898 74.2593 1.1997
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted 1 203.673 182.638 1.11517
    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] Ranked 0 7386.71 6895.44 1.07125
    interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Measured 135.294 149.371 1.10405
    lats homolog 1. [refseq;acc:nm_004690] Rooted 10.2412 9.54479 1.07296
    pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured 1 5894.75 7073.65 1.19999
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared 28896.2 36767 1.27238
    303 60s ribosomal protein l35. [swissprot;acc:p42766] Ranked 242.333 266.999 1.10179
    crk-like protein. [swissprot;acc:p46109] Squared 28896.2 36767 1.27238
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 203.673 182.638 1.11517
    intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Ranked 0 11431.4 12244.1 1.07109
    isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Squared 1487.24 1783.26 1.19904
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Measured 1 22268.8 18560.4 1.1998
    sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 0 952.488 863.886 1.10256
    sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Rooted 10.2412 9.54479 1.07296
    304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Ranked 1 242.339 266.986 1.1017
    40s ribosomal protein s28. [swissprot;acc:p25112] Squared 0 1054.58 879.603 1.19893
    cytohesin 4. [swissprot;acc:q9uia0] Rooted 1 203.673 182.638 1.11517
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Measured 4855.46 5824.52 1.19958
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared 28896.2 36767 1.27238
    rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Rooted 0 31.3568 29.2362 1.07253
    sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Ranked 8021.78 7496.8 1.07003
    ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Measured 4962.34 5469.68 1.10224
    305 40s ribosomal protein s29. [swissprot;acc:p30054] Squared 5295.67 6326.82 1.19472
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Rooted 1 203.673 182.638 1.11517
    ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 0 24.6278 26.4005 1.07198
    microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Ranked 9431 8815 1.06988
    mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] 1 242.339 266.986 1.1017
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Measured 3856.29 4624.15 1.19912
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Squared 28896.2 36767 1.27238
    sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Measured 0 4962.34 5469.68 1.10224
    306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked 1 242.153 266.673 1.10126
    glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Measured 0 1705.19 1547.2 1.10211
    pnas-18. [sptrembl;acc:q9bzu3] 1 13680.5 11409.6 1.19903
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Squared 28896.2 36767 1.27238
    rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Rooted 56.3935 62.8817 1.11505
    scribble. [refseq;acc:nm_015356] 0 18.8966 17.6385 1.07133
    transcription factor btf3 homolog 3. [swissprot;acc:q13892] Squared 31.0895 37.1241 1.1941
    williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Ranked 5540 5921 1.06877
    307 60s ribosomal protein l7. [swissprot;acc:p18124] Squared 5826.27 6955.21 1.19377
    ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Ranked 1091 1021 1.06856

    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
    - 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/