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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1458 to 1507 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    183 ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Divided Squared 79779.8 108084 1.35478
    ANAPC2 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Subtracted 69124.3 54897.4 14226.9
    GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Ranked 227.357 254.15 26.793
    NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided 228.306 198.011 1.153
    NEDD9 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] Rooted 57.4586 66.3336 1.15446
    RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Subtracted 47.6504 36.9304 10.72
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Measured 4241.57 5810.79 1569.22
    184 no value small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Divided Squared 72886.3 98544.5 1.35203
    AIG1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Subtracted Ranked 227.357 254.15 26.793
    ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Divided Rooted 153.602 133.195 1.15321
    CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Subtracted Measured 10804.7 12363.6 1558.9
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Divided Ranked 274.027 237.79 1.15239
    PC pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Subtracted Squared 48127.9 62245.6 14117.7
    RBM15 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Rooted 47.6504 36.9304 10.72
    SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Divided Measured 4069.83 5252.17 1.29051
    185 ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Ranked 281.582 246.371 1.14292
    ATP5F1 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Subtracted 227.357 254.15 26.793
    HGS hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Squared 70830.5 56822 14008.5
    HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Divided Measured 4069.83 5252.17 1.29051
    HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Squared 41502.9 30836.8 1.34589
    MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Rooted 153.578 133.176 1.1532
    PPP2R1B serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Subtracted Measured 4599.26 3058.57 1540.69
    RGS20 regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Rooted 47.6504 36.9304 10.72
    186 COG7 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Squared 70830.5 56822 14008.5
    DNAJC12 j domain containing protein 1. [swissprot;acc:q9ukb3] Ranked 227.357 254.15 26.793
    EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Divided Measured 4071.1 5251.75 1.29001
    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] Ranked 226.582 198.444 1.14179
    Subtracted Measured 4366.44 5899.76 1533.32
    HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Divided Squared 41502.9 30836.8 1.34589
    LBX1 transcription factor lbx1. [swissprot;acc:p52954] Subtracted Rooted 47.6504 36.9304 10.72
    MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided 153.578 133.176 1.1532
    187 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 153.548 133.153 1.15317
    GPSM2 mosaic protein lgn. [swissprot;acc:p81274] Subtracted 47.6504 36.9304 10.72
    HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Divided Squared 41502.9 30836.8 1.34589
    NONO 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Subtracted 71383 57399.3 13983.7
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Divided Ranked 226.582 198.444 1.14179
    Subtracted Measured 4366.44 5899.76 1533.32
    SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Divided 4569.48 5885.79 1.28807
    SNX13 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Subtracted Ranked 227.357 254.15 26.793
    188 E2F1 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] Divided Rooted 46.0352 53.0192 1.15171
    GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Subtracted Ranked 227.357 254.15 26.793
    HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Divided Squared 41502.9 30836.8 1.34589
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Ranked 226.582 198.444 1.14179
    Subtracted Measured 4366.44 5899.76 1533.32
    PSPC1 paraspeckle protein 1. [refseq;acc:nm_018282] Squared 71360.3 57385.8 13974.5
    RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 47.6504 36.9304 10.72
    STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Divided Measured 4571.89 5864.86 1.28281
    189 DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Squared 41502.9 30836.8 1.34589
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Rooted 46.0352 53.0192 1.15171
    GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Subtracted 47.6504 36.9304 10.72

    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/