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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 712 to 761 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    178 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] TFDP2 Rooted 45.7414 52.932 1.1572
    179 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value Ranked 226.884 194.79 1.16476
    mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 Squared 25326.3 18354.1 1.37987
    myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C Measured 21591.5 27904.5 1.29238
    palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] EGFL8 Rooted 50.272 43.4634 1.15665
    180 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] EGFL7 50.2801 43.4779 1.15645
    myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] no value Measured 21591.5 27904.5 1.29238
    plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 Squared 25326.2 18354.1 1.37987
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP Ranked 256.228 298.438 1.16474
    181 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 229.818 267.265 1.16294
    crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] BCAR1 Rooted 57.4432 66.3307 1.15472
    eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 Measured 4068.56 5252.6 1.29102
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 Squared 55630.4 76083.7 1.36766
    182 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] DUT 61733.5 45224.1 1.36506
    histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] HAT1 Ranked 277.546 240.461 1.15422
    rna-binding protein. [refseq;acc:nm_019027] no value Measured 4069.83 5252.17 1.29051
    t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] CCT4 Rooted 57.45 66.332 1.1546
    183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Ranked 228.306 198.011 1.153
    acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] ACADVL Squared 79779.8 108084 1.35478
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value Measured 4069.83 5252.17 1.29051
    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 66.3336 1.15446
    184 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A 153.602 133.195 1.15321
    ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP Measured 4069.83 5252.17 1.29051
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] OSR1 Ranked 274.027 237.79 1.15239
    small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] no value Squared 72886.3 98544.5 1.35203
    185 adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 Ranked 281.582 246.371 1.14292
    c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] HS3ST6 Squared 41502.9 30836.8 1.34589
    heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR Measured 4069.83 5252.17 1.29051
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B Rooted 153.578 133.176 1.1532
    186 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 Measured 4071.1 5251.75 1.29001
    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 226.582 198.444 1.14179
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] HS3ST3A1 Squared 41502.9 30836.8 1.34589
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] MAP1LC3A Rooted 153.578 133.176 1.1532
    187 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B 153.548 133.153 1.15317
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] HS3ST3B1 Squared 41502.9 30836.8 1.34589
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Ranked 226.582 198.444 1.14179
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Measured 4569.48 5885.79 1.28807
    188 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] HS3ST2 Squared 41502.9 30836.8 1.34589
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Ranked 226.582 198.444 1.14179
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Measured 4571.89 5864.86 1.28281
    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 53.0192 1.15171
    189 mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] DCPS Squared 41502.9 30836.8 1.34589
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Measured 4571.89 5864.86 1.28281
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] PRMT8 Ranked 226.582 198.444 1.14179
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 Rooted 46.0352 53.0192 1.15171
    190 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] AQP4 Squared 71389.9 96037.6 1.34525
    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 5864.86 1.28281
    gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] GABARAP Rooted 149.165 129.699 1.15009
    u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] SNRP70 Ranked 226.582 198.444 1.14179
    191 aquaporin 5. [swissprot;acc:p55064] AQP5 Squared 71388.5 96035.2 1.34525

    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/