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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2208 to 2257 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    552 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Rooted 66.082 71.6523 1.08429
    553 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Ranked 207.26 194.346 1.06645
    similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Rooted 66.082 71.6523 1.08429
    tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Measured 3853.64 4379.71 1.13651
    vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Squared 27516.2 32720 1.18912
    554 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Rooted 66.0829 71.6462 1.08419
    pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Measured 14830.5 13050.3 1.13641
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Squared 8426.68 10010.8 1.18799
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Ranked 207.26 194.346 1.06645
    555 proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]
    s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Squared 8426.68 10010.8 1.18799
    selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Measured 6167.93 7007.7 1.13615
    u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Rooted 59.7823 64.7895 1.08376
    556 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Ranked 207.27 194.368 1.06638
    f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Squared 8426.68 10010.8 1.18799
    flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Measured 6167.93 7007.7 1.13615
    signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Rooted 66.0911 71.6061 1.08345
    557 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Squared 8426.68 10010.8 1.18799
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Ranked 207.272 194.371 1.06637
    inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Measured 6167.93 7007.7 1.13615
    t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Rooted 97.1967 105.302 1.08339
    558 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 66.1583 71.6729 1.08335
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Squared 8426.68 10010.8 1.18799
    selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Measured 6167.93 7007.7 1.13615
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Ranked 135.087 144.041 1.06628
    559 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Squared 8426.68 10010.8 1.18799
    ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Rooted 62.7397 67.9651 1.08329
    inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Measured 6167.93 7007.7 1.13615
    neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Ranked 207.309 194.452 1.06612
    560 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Measured 5480.24 6222.04 1.13536
    electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Squared 26334.7 31272.3 1.18749
    putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Rooted 51.0687 47.1439 1.08325
    son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Ranked 205.74 193.021 1.06589
    561 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Rooted 62.7424 67.9648 1.08324
    son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Ranked 205.89 193.183 1.06578
    transforming protein rhoc (h9). [swissprot;acc:p08134] Measured 5480.24 6222.04 1.13536
    u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Squared 18240.1 21659.2 1.18745
    562 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Rooted 62.7424 67.9648 1.08324
    fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Squared 25294.9 30027.4 1.18709
    ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Ranked 220.744 207.121 1.06577
    thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Measured 5480.24 6222.04 1.13536
    563 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
    calcyphosine. [swissprot;acc:q13938] Ranked 220.744 207.121 1.06577
    disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Rooted 62.7424 67.9648 1.08324
    wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Squared 30408.3 36092.8 1.18694
    564 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 25396.2 30143.4 1.18693
    crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Ranked 220.744 207.121 1.06577
    putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Rooted 62.7424 67.9648 1.08324
    transforming protein rhoa (h12). [swissprot;acc:p06749] Measured 5480.24 6222.04 1.13536
    565 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Squared 25287.7 30003.7 1.18649

    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
    - 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/