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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2175 to 2224 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    544 INPP4A Ranked 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] 222.156 208.201 1.06703
    IPO11 Squared ran binding protein 11. [refseq;acc:nm_016338] 26018.9 30994.1 1.19121
    545 AKT2 Measured rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] 3889.27 4426.74 1.13819
    EIF6 Ranked eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 248.866 233.287 1.06678
    FAM57A Squared membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] 26010 30981.7 1.19115
    GABRG2 Rooted gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 66.082 71.6526 1.0843
    546 no value interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]
    ATP5D Squared atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 27162.5 32347.5 1.19089
    WAS Ranked wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 207.222 194.262 1.06671
    ZNF593 Measured zinc finger protein t86. [swissprot;acc:o00488] 4052.77 4612.54 1.13812
    547 CRK Ranked proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 207.26 194.346 1.06645
    GABRA4 Rooted gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 66.082 71.6525 1.0843
    MAT2A Squared s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 25945.4 30892.3 1.19067
    WRNIP1 Measured werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] 5291.92 6020.19 1.13762
    548 ABL2 Ranked tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 207.26 194.346 1.06645
    FDX1 Measured adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 8268.19 9405.85 1.13759
    GABRE Rooted gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 66.082 71.6525 1.0843
    VAMP2 Squared vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] 27516.2 32720 1.18912
    549 no value Ranked proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 207.26 194.346 1.06645
    DPM1 Measured dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] 5865.79 6671.23 1.13731
    JMJD6 Rooted phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 66.082 71.6526 1.0843
    VAMP1 Squared vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] 27516.2 32720 1.18912
    550 GABRA1 Rooted gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 66.082 71.6525 1.0843
    HCK Ranked tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 207.26 194.346 1.06645
    PHB Measured prohibitin. [swissprot;acc:p35232] 5773.45 6563.69 1.13687
    VAMP4 Squared vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] 27516.2 32720 1.18912
    551 no value Measured repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 5773.45 6563.69 1.13687
    CDIPT Squared cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] 27516.2 32720 1.18912
    GABRA3 Rooted gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 66.082 71.6525 1.0843
    GRAP2 Ranked 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] 207.261 194.347 1.06645
    552 ARFGAP1 Squared adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] 27516.2 32720 1.18912
    CRKL Ranked crk-like protein. [swissprot;acc:p46109] 207.26 194.346 1.06645
    CSTF2 Measured cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 15427.2 13572.8 1.13663
    NDUFA6 Rooted nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 66.082 71.6523 1.08429
    553 no value Measured tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 3853.64 4379.71 1.13651
    ABL1 Ranked proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 207.26 194.346 1.06645
    PDXDC1 Rooted similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 66.082 71.6523 1.08429
    VAMP3 Squared vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] 27516.2 32720 1.18912
    554 CLP1 Measured pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 14830.5 13050.3 1.13641
    FYN Ranked proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 207.26 194.346 1.06645
    HOXD9 Rooted homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 66.0829 71.6462 1.08419
    PSEN2 Squared presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 8426.68 10010.8 1.18799
    555 FGR Ranked proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 207.26 194.346 1.06645
    PRPF3 Rooted u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 59.7823 64.7895 1.08376
    SEPHS2 Measured selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 6167.93 7007.7 1.13615
    SKP1A Squared 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] 8426.68 10010.8 1.18799
    556 CBLB Rooted signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 66.0911 71.6061 1.08345
    CUTL1 Ranked ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 207.27 194.368 1.06638
    FBXW7 Squared 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] 8426.68 10010.8 1.18799
    MICAL2 Measured flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 6167.93 7007.7 1.13615

    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/