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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1130 to 1179 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    142 CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted Subtracted 105.205 92.2415 12.9635
    JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 7523.39 1885.19
    PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Divided 9276.47 7090.37 1.30832
    PPIB 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 Subtracted 86600.9 65229.9 21371
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Rooted Divided 55.6161 66.7332 1.19989
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Ranked 59 49 1.20408
    THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 239.99 269.234 29.244
    143 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured Divided 9275.1 7089.65 1.30826
    ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Ranked 59 49 1.20408
    CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Measured Subtracted 15427.2 13572.8 1854.4
    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 65229.9 21371
    PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Divided 124319 86848.2 1.43145
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted 55.6161 66.7332 1.19989
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked Subtracted 240.133 211.382 28.751
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted 105.205 92.2415 12.9635
    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 65229.9 21371
    CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Ranked 239.35 267.915 28.565
    KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Divided 265.686 319.651 1.20312
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 66.7332 1.19989
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Measured Subtracted 4133.47 5945.32 1811.85
    TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Squared Divided 123324 86277.9 1.42938
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Measured 3349.9 4362.61 1.30231
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted Subtracted 105.205 92.2415 12.9635
    145 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 55.6161 66.7332 1.19989
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Squared 310840 442993 1.42515
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 16771.5 12889.1 1.30122
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Rooted Subtracted 105.205 92.2415 12.9635
    COX4I2 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Squared 86600.9 65229.9 21371
    KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked Divided 265.639 319.546 1.20293
    SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Subtracted 239.336 267.881 28.545
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Measured 4136.36 5943.56 1807.2
    146 CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Ranked 239.336 267.879 28.543
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Rooted 41.6734 28.9323 12.7411
    KCNIP2 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] Ranked Divided 265.632 319.531 1.20291
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Rooted 55.0737 66.0298 1.19894
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Squared 103496 146848 1.41888
    STAM2 signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Subtracted 86281 65058.3 21222.7
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Measured Divided 11068 8508.5 1.30082
    XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 2671 871 1800
    147 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Ranked Divided 50.7983 42.3003 1.2009
    ATPBD1C protein x 0004. [refseq;acc:nm_016301] Measured Subtracted 2671 871 1800
    CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided 11068 8508.5 1.30082
    CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Ranked Subtracted 239.32 267.842 28.522
    CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 28.9509 12.7342
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Divided 42.0574 50.4237 1.19893
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Squared Subtracted 55630.4 76083.7 20453.3
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Divided 103496 146848 1.41888
    148 no value ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Subtracted 70011 49783 20228
    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] Ranked 226.582 198.444 28.138
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Rooted Divided 42.0577 50.424 1.19892

    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/