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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 723 to 772 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		network_comparison
    		green
    181 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 Measured 4068.56 1.29102 5252.6
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 Squared 55630.4 1.36766 76083.7
    182 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] DUT 61733.5 1.36506 45224.1
    histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] HAT1 Ranked 277.546 1.15422 240.461
    rna-binding protein. [refseq;acc:nm_019027] no value Measured 4069.83 1.29051 5252.17
    t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] CCT4 Rooted 57.45 1.1546 66.332
    183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Ranked 228.306 1.153 198.011
    acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] ACADVL Squared 79779.8 1.35478 108084
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value Measured 4069.83 1.29051 5252.17
    enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] NEDD9 Rooted 57.4586 1.15446 66.3336
    184 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A 153.602 1.15321 133.195
    ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP Measured 4069.83 1.29051 5252.17
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] OSR1 Ranked 274.027 1.15239 237.79
    small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] no value Squared 72886.3 1.35203 98544.5
    185 adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 Ranked 281.582 1.14292 246.371
    c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] HS3ST6 Squared 41502.9 1.34589 30836.8
    heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR Measured 4069.83 1.29051 5252.17
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B Rooted 153.578 1.1532 133.176
    186 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 Measured 4071.1 1.29001 5251.75
    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 Ranked 226.582 1.14179 198.444
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] HS3ST3A1 Squared 41502.9 1.34589 30836.8
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] MAP1LC3A Rooted 153.578 1.1532 133.176
    187 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B 153.548 1.15317 133.153
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] HS3ST3B1 Squared 41502.9 1.34589 30836.8
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Ranked 226.582 1.14179 198.444
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Measured 4569.48 1.28807 5885.79
    188 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] HS3ST2 Squared 41502.9 1.34589 30836.8
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Ranked 226.582 1.14179 198.444
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Measured 4571.89 1.28281 5864.86
    transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] E2F1 Rooted 46.0352 1.15171 53.0192
    189 mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] DCPS Squared 41502.9 1.34589 30836.8
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Measured 4571.89 1.28281 5864.86
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] PRMT8 Ranked 226.582 1.14179 198.444
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 Rooted 46.0352 1.15171 53.0192
    190 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] AQP4 Squared 71389.9 1.34525 96037.6
    dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] DDOST Measured 4571.89 1.28281 5864.86
    gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] GABARAP Rooted 149.165 1.15009 129.699
    u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] SNRP70 Ranked 226.582 1.14179 198.444
    191 aquaporin 5. [swissprot;acc:p55064] AQP5 Squared 71388.5 1.34525 96035.2
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] no value Ranked 226.582 1.14179 198.444
    pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] PLDN Rooted 63.1192 1.14995 72.584
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Measured 4638.1 1.27712 5923.4
    192 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF 17757.5 1.26767 14008
    aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] AQP2 Squared 71387.4 1.34524 96033.4
    musashi 2 isoform a. [refseq;acc:nm_138962] MSI2 Ranked 227.491 1.14055 199.458
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] SF4 Rooted 53.6107 1.14877 61.5862
    193 lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] MIP Squared 71386.9 1.34524 96032.5
    musashi 1. [refseq;acc:nm_002442] MSI1 Ranked 227.491 1.14055 199.458
    nostrin. [refseq;acc:nm_052946] NOSTRIN Rooted 59.6399 1.1486 51.9242
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 Measured 17756.5 1.26766 14007.3

    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/