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 1458 to 1507 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		network_comparison
    		green
    183 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] ACADVL Divided Squared 79779.8 1.35478 108084
    anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] ANAPC2 Subtracted 69124.3 14226.9 54897.4
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value Divided 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
    glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] GSTO1 Subtracted Ranked 227.357 26.793 254.15
    nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 Measured 4241.57 1569.22 5810.79
    regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] RGS19 Rooted 47.6504 10.72 36.9304
    184 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] AIG1 Ranked 227.357 26.793 254.15
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A Divided Rooted 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
    putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] RBM15 Subtracted Rooted 47.6504 10.72 36.9304
    pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] PC Squared 48127.9 14117.7 62245.6
    small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] no value Divided 72886.3 1.35203 98544.5
    tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] CLEC3B Subtracted Measured 10804.7 1558.9 12363.6
    185 adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 Divided Ranked 281.582 1.14292 246.371
    atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] ATP5F1 Subtracted 227.357 26.793 254.15
    c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] HS3ST6 Divided Squared 41502.9 1.34589 30836.8
    hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] HGS Subtracted 70830.5 14008.5 56822
    heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR Divided 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
    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] RGS20 Subtracted 47.6504 10.72 36.9304
    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] PPP2R1B Measured 4599.26 1540.69 3058.57
    186 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] COG7 Squared 70830.5 14008.5 56822
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 Divided 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
    Subtracted Measured 4366.44 1533.32 5899.76
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] HS3ST3A1 Divided Squared 41502.9 1.34589 30836.8
    j domain containing protein 1. [swissprot;acc:q9ukb3] DNAJC12 Subtracted Ranked 227.357 26.793 254.15
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] MAP1LC3A Divided Rooted 153.578 1.1532 133.176
    transcription factor lbx1. [swissprot;acc:p52954] LBX1 Subtracted 47.6504 10.72 36.9304
    187 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] NONO Squared 71383 13983.7 57399.3
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B Divided Rooted 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
    mosaic protein lgn. [swissprot;acc:p81274] GPSM2 Subtracted Rooted 47.6504 10.72 36.9304
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Divided Ranked 226.582 1.14179 198.444
    Subtracted Measured 4366.44 1533.32 5899.76
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Divided 4569.48 1.28807 5885.79
    sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] SNX13 Subtracted Ranked 227.357 26.793 254.15
    188 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] HS3ST2 Divided Squared 41502.9 1.34589 30836.8
    paraspeckle protein 1. [refseq;acc:nm_018282] PSPC1 Subtracted 71360.3 13974.5 57385.8
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Divided Ranked 226.582 1.14179 198.444
    Subtracted Measured 4366.44 1533.32 5899.76
    regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] RGS17 Rooted 47.6504 10.72 36.9304
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Divided 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 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] PCYT1A Subtracted Ranked 241.373 25.979 267.352
    guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] GNAO1 Rooted 47.6504 10.72 36.9304
    mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] DCPS Divided Squared 41502.9 1.34589 30836.8

    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/