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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2151 to 2200 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    269 SOAT1 sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610] Ranked Low confidence 208.436 199.44 1.04511
    TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Rooted 70.8256 74.7762 1.05578
    270 C16orf80 transcription factor iib. [refseq;acc:nm_013242] Squared High confidence 64739.9 50300.6 1.28706
    CPA5 carboxypeptidase a5. [refseq;acc:nm_080385] Measured Low confidence 8811.88 9345.51 1.06056
    CRKL crk-like protein. [swissprot;acc:p46109] Rooted High confidence 66.1064 74.1074 1.12103
    EDEM2 putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94] Low confidence 72.3095 76.336 1.05568
    FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured High confidence 23640.2 19479.8 1.21358
    FLAD1 fad synthetase. [refseq;acc:nm_025207] Ranked 241.373 267.352 1.10763
    RNF10 ring finger protein 10. [refseq;acc:nm_014868] Low confidence 208.437 199.44 1.04511
    UTP3 disrupter of silencing 10. [refseq;acc:nm_020368] Squared 51294.5 47142.5 1.08807
    271 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Ranked High confidence 241.373 267.352 1.10763
    ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Rooted 66.1064 74.1073 1.12103
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Measured 2554.89 3093.78 1.21092
    CPB1 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Low confidence 8811.69 9345.26 1.06055
    PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Squared 51583 47416 1.08788
    SFRS8 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] High confidence 64739.9 50300.6 1.28706
    SPSB4 spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] Rooted Low confidence 65.1441 68.7656 1.05559
    TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Ranked 201.219 192.595 1.04478
    272 ALDH4A1 delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Measured 11162 10526.2 1.0604
    AP2A2 adapter-related protein complex 2 alpha 2 subunit (alpha-adaptin c) (clathrin assembly protein complex 2 alpha-c large chain) (100 kda coated vesicle protein c) (plasma membrane adaptor ha2/ap2 adaptin alpha c subunit) (huntingtin-interacting protein hypj). [swissprot;acc:o94973] Rooted 70.162 74.0605 1.05556
    FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Squared High confidence 36563.7 46971.1 1.28464
    FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Rooted 66.1064 74.1074 1.12103
    HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Measured 3858.52 4669.27 1.21012
    LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked 241.373 267.352 1.10763
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Low confidence 217.69 208.421 1.04447
    PPP1CC serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 51555.9 47412 1.0874
    273 CDC73 parafibromin. [refseq;acc:nm_024529] Ranked 214.015 204.916 1.0444
    EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured High confidence 3199.4 3870.8 1.20985
    FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Rooted 66.1064 74.1074 1.12103
    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] Squared 16120.1 20665.7 1.28198
    HOOK3 golgi-associated microtubule-binding protein hook3; hook3 protein. [refseq;acc:nm_032410] Low confidence 49860 45859.7 1.08723
    PAPSS1 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Ranked High confidence 241.373 267.352 1.10763
    PLAA phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Measured Low confidence 11162 10526.2 1.0604
    PUF60 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Rooted 70.162 74.0605 1.05556
    274 AP2S1 clathrin coat assembly protein ap17 (clathrin coat associated protein ap17) (plasma membrane adaptor ap-2 17 kda protein) (ha2 17 kda subunit) (clathrin assembly protein 2 small chain). [swissprot;acc:p53680]
    GRAP2 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] High confidence 66.1063 74.1068 1.12102
    HOOK1 hook1 protein. [refseq;acc:nm_015888] Squared Low confidence 49842 45846.9 1.08714
    KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked 209.532 200.653 1.04425
    POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] High confidence 241.373 267.352 1.10763
    RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Measured 3119.98 2579.49 1.20953
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Squared 16120.1 20665.7 1.28198
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Measured Low confidence 7718.85 8184.75 1.06036
    275 no value adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782] Rooted 70.162 74.0605 1.05556
    CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] High confidence 66.1048 74.0977 1.12091
    GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Measured Low confidence 7506.19 7958.12 1.06021
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked 199.66 191.203 1.04423
    PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] High confidence 241.373 267.352 1.10763
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Squared 16120.1 20665.7 1.28198
    RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Measured 3119.98 2579.49 1.20953
    TTK dual specificity protein kinase ttk (ec 2.7.1.-) (pyt). [swissprot;acc:p33981] Squared Low confidence 47648.2 43829.4 1.08713

    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/