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 red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 258 to 307 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		green
    		network_comparison
    129 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 Divided 94 114 1.21277
    130 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] EGFL8 Subtracted 242.735 276.059 33.324
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A Divided 94 114 1.21277
    131 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] EGFL7 Subtracted 242.718 276.018 33.3
    son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] SON Divided 294.053 242.562 1.21228
    132 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] NCBP2L Subtracted 229.406 196.695 32.711
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 Divided 350 290 1.2069
    133 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] no value Subtracted 226.887 194.72 32.167
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] TOB1 Divided 350 290 1.2069
    134 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value Subtracted 226.884 194.79 32.094
    135 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 Divided 350 290 1.2069
    forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] FOXP4 Subtracted 263.215 231.407 31.808
    136 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 Divided 350 290 1.2069
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] FOXP1 Subtracted 263.215 231.407 31.808
    137 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] FOXP3 263.191 231.394 31.797
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 Divided 350 290 1.2069
    138 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] TIPRL Subtracted 174.667 205.556 30.889
    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 Divided 194.372 234.204 1.20493
    139 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] APBA1 271.752 225.68 1.20415
    chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] CHRAC1 Subtracted 287.41 256.835 30.575
    140 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 228.306 198.011 30.295
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Divided 59 49 1.20408
    141 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP Subtracted 239.991 269.238 29.247
    ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC Divided 59 49 1.20408
    142 ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB
    thrombospondin 3 precursor. [swissprot;acc:p49746] THBS3 Subtracted 239.99 269.234 29.244
    143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN Divided 59 49 1.20408
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] SF4 Subtracted 240.133 211.382 28.751
    144 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] CSRP1 239.35 267.915 28.565
    kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] KCNIP1 Divided 265.686 319.651 1.20312
    145 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] SHCBP1 Subtracted 239.336 267.881 28.545
    potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] KCNIP4 Divided 265.639 319.546 1.20293
    146 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 265.632 319.531 1.20291
    smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] CSRP2 Subtracted 239.336 267.879 28.543
    147 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] CSRP3 239.32 267.842 28.522
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value Divided 50.7983 42.3003 1.2009
    148 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 Subtracted 226.582 198.444 28.138
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A Divided 296.677 247.559 1.19841
    149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value 142 170 1.19718
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Subtracted 226.582 198.444 28.138
    150 myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B Divided 55 46 1.19565
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Subtracted 226.582 198.444 28.138
    151 myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C Divided 55 46 1.19565
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] PRMT8 Subtracted 226.582 198.444 28.138
    152 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] no value Divided 55 46 1.19565
    u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] SNRP70 Subtracted 226.582 198.444 28.138
    153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] RBM15B Divided 249.663 298.263 1.19466
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] no value Subtracted 226.582 198.444 28.138
    154 musashi 2 isoform a. [refseq;acc:nm_138962] MSI2 227.491 199.458 28.033

    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/