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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type red Interaction Map Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 1851 to 1900 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] 3184 SP100 0.00001 1 0.00001
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 147 no value 50.7983 1.2009 42.3003
    nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] 2743 NFE2L3 198.278 1.00022 198.321
    nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494] 2742 NFE2L1
    nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] 2654 NFKB2 201.452 1.0011 201.674
    nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] 2652 NFKB1 201.451 201.673
    nuclear factor related to kappa b binding protein. [refseq;acc:nm_006165] 2823 NFRKB 0.00001 1 0.00001
    nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] 1946 NFIL3 214.234 1.00986 212.142
    nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] 1623 NUFIP1 228.611 1.01521 225.185
    nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] 2135 NR4A3 207.743 1.00696 206.308
    nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] 2507 PPP1R8 151.386 1.0025 151.009
    nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 531 PRPF19 223.356 1.06793 209.149
    nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658] 3008 NUP214 0.00001 1 0.00001
    nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] 997 NUP88 219.656 1.03345 212.547
    nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] 1576 NUP98 222.585 1.01645 218.982
    nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 690 SNW1 220.593 1.05553 208.987
    nuclear protein ukp68. [refseq;acc:nm_024824] 194 ZC3H14 227.491 1.14055 199.458
    nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 2521 no value 201.96 1.00234 201.488
    nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782] 2059 NCOA7 218.79 1.00834 216.981
    nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 1123 NXF1 169.031 1.0275 164.507
    nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 1118 NXF3 168.995 1.02753 164.467
    nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 1117 NXF5 168.989 1.02754 164.46
    nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 291 NFYB 251.679 1.10368 228.037
    nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 35 NFYC 260.532 1.27519 204.309
    nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662] 3113 NUTF2 0.00001 1 0.00001
    nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991] 2683 YBX1 208.438 1.00095 208.635
    nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 1877 NUCB1 212.186 1.01075 214.467
    nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 1879 NUCB2
    nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 491 GTPBP4 251.83 1.07184 234.951
    nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [swissprot;acc:q14978] 2842 NOLC1 0.00001 1 0.00001
    nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 479 NOLA1 228.051 1.07409 212.321
    nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] 1734 NOLA2 221.921 1.01296 219.081
    nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] 1127 no value 239.219 1.02741 232.837
    nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 719 NOL5A 247.769 1.054 235.074
    nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] 934 NOL6 242.024 1.03631 233.544
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 170 TIA1 227.199 1.17894 192.715
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 171 TIAL1 227.202 1.17829 192.823
    nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748] 2785 NPM1 0.00001 1 0.00001
    nucleoplasmin 3. [swissprot;acc:o75607] 3096 NPM3
    nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [swissprot;acc:q9ukx7] 3154 NUP50
    nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426] 1671 NUP54 228.496 1.01415 231.729
    nucleoporin like 1. [refseq;acc:nm_014089] 1776 NUPL1 216.878 1.0121 214.286
    nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 1826 NUP43 202.393 1.01149 200.094
    nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] 639 HRB 217.67 1.05938 230.596
    nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 1827 NME3 191.39 1.01147 189.219
    nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] 1797 NME2 193.111 1.01193 190.834
    nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] 1794 no value 193.138 190.861
    nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209] 2757 NAP1L1 0.00001 1 0.00001
    nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6] 2758 NAP1L2
    nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 3080 no value

    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/