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 Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1112 to 1161 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Value Type
    		red
    		network_comparison
    		green
    139 ZC3H14 Divided nuclear protein ukp68. [refseq;acc:nm_024824] Rooted 54.9787 1.20486 66.2416
    140 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Squared 81527.6 1.45091 56190.6
    FLNB 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] Rooted 55.6161 1.19989 66.7332
    HLX Subtracted homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Measured 2597.5 1899 698.5
    KCNIP2 Divided 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] 2760.28 1.31425 2100.27
    NCBP2 Subtracted 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Ranked 228.306 30.295 198.011
    PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Squared 86609.4 21374.9 65234.5
    RRAGA Divided ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Ranked 59 1.20408 49
    UNC84A Subtracted sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Rooted 39.9725 13.0248 52.9973
    141 CCNB1 Divided g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared 81520.8 1.45084 56188.5
    COMP Subtracted cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Ranked 239.991 29.247 269.238
    HBS1L hbs1-like. [refseq;acc:nm_006620] Measured 2597.5 1899 698.5
    PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Squared 86600.9 21371 65229.9
    REV1 Divided rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Rooted 55.6161 1.19989 66.7332
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Ranked 59 1.20408 49
    SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Measured 4405.4 1.3125 5782.08
    STAMBPL1 Subtracted associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Rooted 105.205 12.9635 92.2415
    142 CDC2 Divided cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Squared 81478.9 1.45044 56175.2
    CHMP2A Subtracted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted 105.205 12.9635 92.2415
    JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 1885.19 7523.39
    PITRM1 Divided metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 1.30832 7090.37
    PPIB Subtracted peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Squared 86600.9 21371 65229.9
    PRMT1 Divided protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Rooted 55.6161 1.19989 66.7332
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Ranked 59 1.20408 49
    THBS3 Subtracted thrombospondin 3 precursor. [swissprot;acc:p49746] 239.99 29.244 269.234
    143 ALG1 Divided beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured 9275.1 1.30826 7089.65
    ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Ranked 59 1.20408 49
    CSTF2 Subtracted cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Measured 15427.2 1854.4 13572.8
    OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Squared 86600.9 21371 65229.9
    PPP1R13B Divided protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 124319 1.43145 86848.2
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted 55.6161 1.19989 66.7332
    SF4 Subtracted splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked 240.133 28.751 211.382
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted 105.205 12.9635 92.2415
    144 COX4I1 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Squared 86600.9 21371 65229.9
    CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Ranked 239.35 28.565 267.915
    KCNIP1 Divided kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 265.686 1.20312 319.651
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 1.19989 66.7332
    TIA1 Subtracted nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Measured 4133.47 1811.85 5945.32
    TP53BP2 Divided tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Squared 123324 1.42938 86277.9
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Measured 3349.9 1.30231 4362.61
    VPS24 Subtracted neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted 105.205 12.9635 92.2415
    145 no value Divided filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 55.6161 1.19989 66.7332
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Squared 310840 1.42515 442993
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 16771.5 1.30122 12889.1
    CHMP4A Subtracted protein hspc134 (protein cda04). [swissprot;acc:q9by43] Rooted 105.205 12.9635 92.2415
    COX4I2 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Squared 86600.9 21371 65229.9
    KCNIP4 Divided potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked 265.639 1.20293 319.546
    SHCBP1 Subtracted likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 239.336 28.545 267.881
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Measured 4136.36 1807.2 5943.56
    146 CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Ranked 239.336 28.543 267.879

    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/