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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1108 to 1157 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    139 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] CCNB2 Squared Divided 81592.1 56211.1 1.45153
    nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 Rooted 54.9787 66.2416 1.20486
    potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] KCNIP4 Measured 2759.61 2099.49 1.31442
    signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] STAM Squared Subtracted 86861.5 65369.7 21491.8
    voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] CACNG5 Rooted 49.3267 62.4167 13.09
    140 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Ranked 228.306 198.011 30.295
    cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] CDK2 Squared Divided 81527.6 56190.6 1.45091
    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 Rooted 55.6161 66.7332 1.19989
    homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] HLX Measured Subtracted 2597.5 698.5 1899
    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 Divided 2760.28 2100.27 1.31425
    protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] PRKCH Squared Subtracted 86609.4 65234.5 21374.9
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Ranked Divided 59 49 1.20408
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A Rooted Subtracted 39.9725 52.9973 13.0248
    141 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 105.205 92.2415 12.9635
    cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP Ranked 239.991 269.238 29.247
    g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] CCNB1 Squared Divided 81520.8 56188.5 1.45084
    hbs1-like. [refseq;acc:nm_006620] HBS1L Measured Subtracted 2597.5 698.5 1899
    protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] PRKCE Squared 86600.9 65229.9 21371
    ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC Ranked Divided 59 49 1.20408
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Rooted 55.6161 66.7332 1.19989
    small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 Measured 4405.4 5782.08 1.3125
    142 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] CDC2 Squared 81478.9 56175.2 1.45044
    metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] PITRM1 Measured 9276.47 7090.37 1.30832
    peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] PPIB Squared Subtracted 86600.9 65229.9 21371
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Rooted Divided 55.6161 66.7332 1.19989
    putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] CHMP2A Subtracted 105.205 92.2415 12.9635
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Ranked Divided 59 49 1.20408
    thrombospondin 3 precursor. [swissprot;acc:p49746] THBS3 Subtracted 239.99 269.234 29.244
    transcription factor jun-d. [swissprot;acc:p17535] JUND Measured 5638.2 7523.39 1885.19
    143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN Ranked Divided 59 49 1.20408
    associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP Rooted Subtracted 105.205 92.2415 12.9635
    beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] ALG1 Measured Divided 9275.1 7089.65 1.30826
    cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] CSTF2 Subtracted 15427.2 13572.8 1854.4
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] PRMT8 Rooted Divided 55.6161 66.7332 1.19989
    protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] PPP1R13B Squared 124319 86848.2 1.43145
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] SF4 Ranked Subtracted 240.133 211.382 28.751
    udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] OGT Squared 86600.9 65229.9 21371
    144 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] CSRP1 Ranked 239.35 267.915 28.565
    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] COX4I1 Squared 86600.9 65229.9 21371
    kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] KCNIP1 Ranked Divided 265.686 319.651 1.20312
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 Rooted Subtracted 105.205 92.2415 12.9635
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 Measured 4133.47 5945.32 1811.85
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A Divided 3349.9 4362.61 1.30231
    tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] TP53BP2 Squared 123324 86277.9 1.42938
    u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] SNRP70 Rooted 55.6161 66.7332 1.19989
    145 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] COX4I2 Squared Subtracted 86600.9 65229.9 21371
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] no value Rooted Divided 55.6161 66.7332 1.19989
    likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] SHCBP1 Ranked Subtracted 239.336 267.881 28.545
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value Squared Divided 310840 442993 1.42515
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 Measured Subtracted 4136.36 5943.56 1807.2

    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/