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 5964 to 6013 of 14920 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    989 signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Measured 11743.3 10712.3 1.09624
    990 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Ranked 243.297 235.373 1.03367
    dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Measured 5147.9 5641.25 1.09584
    dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] Squared 23339.9 26834.1 1.14971
    orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Rooted 64.0581 67.5829 1.05503
    991 aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] Squared 26705.9 30699 1.14952
    dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Ranked 203.381 196.76 1.03365
    transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Measured 6472.38 7092.65 1.09583
    u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Rooted 52.2349 55.1039 1.05492
    992 lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Squared 18885.2 21708.3 1.14949
    mstp028 protein. [refseq;acc:nm_031954] Rooted 61.7824 65.1711 1.05485
    putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Measured 5393.37 5909.47 1.09569
    serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Ranked 218.468 211.357 1.03364
    993 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Measured 6499.89 7121.77 1.09568
    peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Squared 29881.4 34348 1.14948
    pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Ranked 211.071 204.205 1.03362
    swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Rooted 61.7884 65.1721 1.05476
    994 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] Measured 5800.95 6355.71 1.09563
    poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Ranked 116.845 120.772 1.03361
    pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Squared 18761.8 21564.5 1.14938
    tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Rooted 61.7917 65.1727 1.05472
    995 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] Measured 5778.65 6328.56 1.09516
    dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Squared 25141.4 28896.8 1.14937
    mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Ranked 219.656 212.547 1.03345
    polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Rooted 61.7923 65.1728 1.05471
    996 j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 69.5394 73.3277 1.05448
    lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Squared 25141.4 28896.8 1.14937
    methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Measured 5110.6 5596.73 1.09512
    mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Ranked 219.656 212.547 1.03345
    997 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Rooted 69.5394 73.3277 1.05448
    lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] Squared 25141.4 28896.8 1.14937
    nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Ranked 219.656 212.547 1.03345
    nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] Measured 5144.74 5634 1.0951
    998 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Ranked 225.557 218.271 1.03338
    mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Squared 25141.4 28896.8 1.14937
    transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] Measured 5144.74 5634 1.0951
    zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Rooted 69.5394 73.3277 1.05448
    999 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
    lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] Squared 25141.4 28896.8 1.14937
    triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Measured 5680.76 6220.45 1.095
    vinculin (metavinculin). [swissprot;acc:p18206] Ranked 215.92 208.95 1.03336
    1000 ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Measured 5680.76 6220.45 1.095
    heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Squared 27225.4 31287.9 1.14922
    kinesin protein. [refseq;acc:nm_032559] Rooted 59.2757 62.5044 1.05447
    sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Ranked 225.167 217.922 1.03325
    1001 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Rooted 67.7551 71.4422 1.05442
    enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Squared 21068.2 24205.2 1.1489
    lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Measured 5680.76 6220.45 1.095
    sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Ranked 225.167 217.922 1.03325
    1002 40s ribosomal protein s30. [swissprot;acc:q05472] Rooted 61.3513 64.6874 1.05438

    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/