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 Gene Rank Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1862 to 1911 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 531 PRPF19 223.356 209.149 1.06793
    nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658] 3008 NUP214 0.00001 0.00001 1
    nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] 997 NUP88 219.656 212.547 1.03345
    nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] 1576 NUP98 222.585 218.982 1.01645
    nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 690 SNW1 220.593 208.987 1.05553
    nuclear protein ukp68. [refseq;acc:nm_024824] 194 ZC3H14 227.491 199.458 1.14055
    nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 2521 no value 201.96 201.488 1.00234
    nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782] 2059 NCOA7 218.79 216.981 1.00834
    nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 1123 NXF1 169.031 164.507 1.0275
    nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 1118 NXF3 168.995 164.467 1.02753
    nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 1117 NXF5 168.989 164.46 1.02754
    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 251.679 228.037 1.10368
    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 260.532 204.309 1.27519
    nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662] 3113 NUTF2 0.00001 0.00001 1
    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 208.438 208.635 1.00095
    nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 1877 NUCB1 212.186 214.467 1.01075
    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 251.83 234.951 1.07184
    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 0.00001 1
    nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 479 NOLA1 228.051 212.321 1.07409
    nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] 1734 NOLA2 221.921 219.081 1.01296
    nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] 1127 no value 239.219 232.837 1.02741
    nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 719 NOL5A 247.769 235.074 1.054
    nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] 934 NOL6 242.024 233.544 1.03631
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 170 TIA1 227.199 192.715 1.17894
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 171 TIAL1 227.202 192.823 1.17829
    nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748] 2785 NPM1 0.00001 0.00001 1
    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 228.496 231.729 1.01415
    nucleoporin like 1. [refseq;acc:nm_014089] 1776 NUPL1 216.878 214.286 1.0121
    nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 1826 NUP43 202.393 200.094 1.01149
    nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] 639 HRB 217.67 230.596 1.05938
    nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 1827 NME3 191.39 189.219 1.01147
    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 193.111 190.834 1.01193
    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 0.00001 1
    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
    nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 518 GNL3 250.858 234.563 1.06947
    nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 672 NUBP2 210.739 199.398 1.05688
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 671 NUBP1
    nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] 370 NUDT12 242.159 265.104 1.09475
    numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] 968 NUMB 211.987 204.964 1.03426
    numb-like protein (numb-r). [swissprot;acc:q9y6r0] 972 NUMBL
    ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] 2045 C19orf29 199.928 198.24 1.00851
    ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] 1205 KIF21A 224.805 219.251 1.02533
    o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] 1717 OSGEP 221.058 218.164 1.01327
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 184 OSR1 274.027 237.79 1.15239
    oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 224 SLC15A2 185.969 165.623 1.12285

    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/