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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1151 to 1200 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    144 Rooted ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] RPS6KC1 Low confidence 1.06928 71.2226 76.1572
    u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] SNRP70 High confidence 1.19989 55.6161 66.7332
    145 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 Low confidence 1.08741 7693.93 8366.42
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] no value High confidence 1.30122 16771.5 12889.1
    Ranked potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] KCNIP4 1.20293 265.639 319.546
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 Low confidence 1.06201 211.056 198.732
    Squared filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] FLNB 1.13016 51943.5 45961.2
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value High confidence 1.42515 310840 442993
    Rooted dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] DNAJC8 Low confidence 1.06909 64.627 69.0919
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] no value High confidence 1.19989 55.6161 66.7332
    146 Measured associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 1.30082 11068 8508.5
    pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] PANK3 Low confidence 1.08679 10685.5 11612.9
    Ranked kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] KCNIP2 High confidence 1.20291 265.632 319.531
    nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] NDUFS4 Low confidence 1.06193 226.892 213.661
    Squared ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA High confidence 1.41888 103496 146848
    syntaxin binding protein 1 (unc-18 homolog) (unc-18a) (unc-18-1) (n- sec1) (rbsec1) (p67). [swissprot;acc:q64320] STXBP1 Low confidence 1.12944 74200.8 65696.9
    Rooted c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] GGNBP2 1.06909 64.627 69.0919
    huntingtin interacting protein c. [refseq;acc:nm_012272] PRPF40B High confidence 1.19894 55.0737 66.0298
    147 Measured pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] PANK2 Low confidence 1.08677 10684.1 11611.2
    putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] CHMP2A High confidence 1.30082 11068 8508.5
    Ranked nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value 1.2009 50.7983 42.3003
    rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] ARHGEF6 Low confidence 1.06182 219.273 206.507
    Squared prohibitin. [swissprot;acc:p35232] PHB 1.12825 73503.9 82930.5
    ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC High confidence 1.41888 103496 146848
    Rooted forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] FOXP4 1.19893 42.0574 50.4237
    transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] TAGLN Low confidence 1.06891 65.5094 70.0235
    148 Measured associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP High confidence 1.30082 11068 8508.5
    defender against cell death 1 (dad-1). [swissprot;acc:p46966] DAD1 Low confidence 1.08675 6893.42 7491.39
    Ranked sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A High confidence 1.19841 296.677 247.559
    sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] SENP8 Low confidence 1.06176 210.579 198.33
    Squared abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] ABI2 1.12457 53637.6 47696
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB High confidence 1.41888 103496 146848
    Rooted forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] FOXP1 1.19892 42.0577 50.424
    neuronal protein np25. [swissprot;acc:q9ui15] TAGLN3 Low confidence 1.06868 65.4595 69.9554
    149 Measured neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 High confidence 1.30082 11068 8508.5
    pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] PANK1 Low confidence 1.08647 10665 11587.2
    Ranked atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value High confidence 1.19718 142 170
    ubiquitin-like protein nedd8. [swissprot;acc:q15843] NEDD8 Low confidence 1.06176 210.579 198.33
    Squared anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN High confidence 1.41888 103496 146848
    ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] RNF40 Low confidence 1.12445 54898 48821.9
    Rooted forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] FOXP3 High confidence 1.19882 42.0684 50.4323
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value Low confidence 1.06862 101.348 108.302
    150 Measured protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A High confidence 1.30082 11068 8508.5
    serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] PLK1 Low confidence 1.08628 7136.14 7751.87
    Ranked myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B High confidence 1.19565 55 46
    serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] PLK1 Low confidence 1.06148 206.516 194.554
    Squared cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] CSTF3 1.12431 55463.4 49331.1
    pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] CLP1 High confidence 1.41799 121200 85473.4
    Rooted homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Low confidence 1.06862 101.348 108.302
    serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] PPP2CA High confidence 1.19774 63.5827 53.0856

    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/