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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 570 to 619 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    Hugo
    description
    Network Comparison Type
    Interaction Map
    red
    green
    network_comparison
    143 FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Subtracted Low confidence 211.056 198.732 12.324
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 1.06201
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Subtracted High confidence 240.133 211.382 28.751
    144 CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 28.565
    FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Divided Low confidence 211.056 198.732 1.06201
    KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 265.686 319.651 1.20312
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted Low confidence 211.056 198.732 12.324
    145 KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Divided High confidence 265.639 319.546 1.20293
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Low confidence 211.056 198.732 1.06201
    SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Subtracted 210.579 198.33 12.249
    SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] High confidence 239.336 267.881 28.545
    146 CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 267.879 28.543
    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] Divided 265.632 319.531 1.20291
    NDUFS4 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] Low confidence 226.892 213.661 1.06193
    NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Subtracted 210.579 198.33 12.249
    147 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided High confidence 50.7983 42.3003 1.2009
    ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 219.273 206.507 1.06182
    CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Subtracted 222.508 210.345 12.163
    CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] High confidence 239.32 267.842 28.522
    148 CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Low confidence 222.502 210.342 12.16
    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] High confidence 226.582 198.444 28.138
    SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Divided Low confidence 210.579 198.33 1.06176
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] High confidence 296.677 247.559 1.19841
    149 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718
    HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Subtracted Low confidence 202.996 190.854 12.142
    NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Divided 210.579 198.33 1.06176
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Subtracted High confidence 226.582 198.444 28.138
    150 CTSL2 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Low confidence 211.818 199.734 12.084
    MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Divided High confidence 55 46 1.19565
    PLK1 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Low confidence 206.516 194.554 1.06148
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Subtracted High confidence 226.582 198.444 28.138
    151 CTSZ cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Divided Low confidence 206.516 194.554 1.06148
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Subtracted 191.688 179.639 12.049
    MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Divided High confidence 55 46 1.19565
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Subtracted 226.582 198.444 28.138
    152 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Divided 55 46 1.19565
    CTSL1 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Subtracted Low confidence 211.808 199.761 12.047
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Divided 202.934 191.187 1.06144
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Subtracted High confidence 226.582 198.444 28.138
    153 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
    PLK1 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Low confidence 206.516 194.554 11.962
    RAB11FIP4 rab11-family interacting protein 4. [refseq;acc:nm_032932] Divided 183.27 172.702 1.06119
    RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] High confidence 249.663 298.263 1.19466
    154 CTSZ cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Subtracted Low confidence 206.516 194.554 11.962
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] High confidence 227.491 199.458 28.033
    RAB11FIP3 eferin. [swissprot;acc:o75154] Divided Low confidence 183.27 172.702 1.06119
    RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] High confidence 249.663 298.263 1.19466
    155 CTSL2 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Low confidence 211.818 199.734 1.0605
    MSI1 musashi 1. [refseq;acc:nm_002442] Subtracted High confidence 227.491 199.458 28.033
    RBM15 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided 249.663 298.263 1.19466

    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/