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 Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 12864 to 12913 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    804 TST Subtracted Squared thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] High confidence 19987.6 23960.7 3973.1
    805 no value Divided Measured 60s ribosomal protein l39. [swissprot;acc:p02404] 4708.61 5226.71 1.11003
    Rooted 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 74.3557 79.1513 1.0645
    Subtracted Ranked early hematopoietic zinc finger. [refseq;acc:nm_015461] Low confidence 204.914 199.706 5.208
    ANKRA2 Divided ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] High confidence 212.386 221.785 1.04425
    IFRD1 Subtracted Measured interferon-related developmental regulator 1 (nerve growth factor- inducible protein pc4). [swissprot;acc:o00458] Low confidence 7709.38 8035.7 326.32
    INPP4A Divided 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] 7837.99 8162.73 1.04143
    MLF1 Subtracted Rooted myeloid leukemia factor 1 (myelodysplasia-myeloid leukemia factor 1). [swissprot;acc:p58340] 73.7693 76.7095 2.9402
    MPST Squared 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] High confidence 19987.6 23960.7 3973.1
    NEUROD1 Measured neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 779.167 1390.33 611.163
    POLE Divided Squared dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 15384.8 17890 1.16284
    PTPRB Subtracted Rooted protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 82.184 86.2753 4.0913
    RFXANK Ranked dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] 212.386 221.785 9.399
    SNX16 Divided Squared sorting nexin 16. [swissprot;acc:p57768] Low confidence 43910.5 41772.3 1.05119
    SUPT16H Rooted chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] 72.0306 74.9692 1.0408
    SYNJ1 Ranked synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] 198.496 193.399 1.02635
    TXNDC9 Subtracted Squared protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 45872.2 43667.8 2204.4
    806 no value Divided Measured 60s ribosomal protein l18a. [swissprot;acc:q02543] High confidence 4708.61 5226.71 1.11003
    Rooted 40s ribosomal protein s26. [swissprot;acc:p02383] 62.4161 58.6426 1.06435
    ATP6V1C1 Ranked vacuolar atp synthase subunit c (ec 3.6.3.14) (v-atpase c subunit) (vacuolar proton pump c subunit). [swissprot;acc:p21283] Low confidence 202.369 197.173 1.02635
    CNIH4 Subtracted Rooted protein hspc163. [swissprot;acc:q9p003] 75.9558 78.896 2.9402
    GPI Divided Squared glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] 47813.4 45485.5 1.05118
    GPR84 Ranked inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] High confidence 212.386 221.785 1.04425
    GPSM2 Subtracted mosaic protein lgn. [swissprot;acc:p81274] Low confidence 207.56 202.355 5.205
    GSTZ1 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] High confidence 267.447 276.773 9.326
    HTATIP Squared 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] Low confidence 46282.7 44079.6 2203.1
    IMPA1 Divided inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] High confidence 25555.4 29715.4 1.16278
    LSM5 Subtracted Measured u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Low confidence 7934.34 8260.54 326.2
    MAPKAPK2 Divided map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] 8379.95 8726.61 1.04137
    NEUROD4 Subtracted neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence 779.167 1390.33 611.163
    PRSS16 Rooted thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 82.184 86.2753 4.0913
    RHOA Squared transforming protein rhoa (h12). [swissprot;acc:p06749] 19987.6 23960.7 3973.1
    WNK1 Divided Rooted protein kinase, lysine deficient 1; kinase deficient protein. [refseq;acc:nm_018979] Low confidence 70.5871 73.4673 1.0408
    807 no value exonuclease nef-sp. [refseq;acc:nm_030941]
    CBS Squared cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 47169.4 44873.3 1.05117
    CCDC47 Subtracted Rooted gk001 protein. [refseq;acc:nm_020198] High confidence 82.184 86.2753 4.0913
    CHD5 Measured chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 779.167 1390.33 611.163
    COPG Divided coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Low confidence 8272.57 8614.36 1.04132
    GART Subtracted Ranked trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] High confidence 218.521 227.796 9.275
    GLI1 Squared zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Low confidence 46721 44519 2202
    IMPA2 Divided inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] High confidence 25560.1 29720.6 1.16277
    ME3 Subtracted Measured nadp-dependent malic enzyme, mitochondrial precursor (ec 1.1.1.40) (nadp-me) (malic enzyme 3). [swissprot;acc:q16798] Low confidence 8275.91 8602.07 326.16
    MXD1 Squared mad protein (max dimerizer). [swissprot;acc:q05195] High confidence 17248.4 21214 3965.6
    NFYB Ranked nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Low confidence 203.907 198.706 5.201
    PNKD Divided myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] 200.782 195.631 1.02633
    PPT1 palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] High confidence 212.386 221.785 1.04425
    RPS19 Measured 40s ribosomal protein s19. [swissprot;acc:p39019] 4708.61 5226.71 1.11003
    SUPT16H Subtracted Rooted chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Low confidence 72.0306 74.9692 2.9386
    TIMM22 Divided mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] High confidence 62.416 58.6426 1.06435
    808 ATP2C1 Subtracted calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 65.1843 69.2736 4.0893

    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/