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 Network Comparison Type Hugo Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 8191 to 8240 of 66312 in total
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    512 Subtracted SLC7A5 Measured large neutral amino acids transporter small subunit 1 (l-type amino acid transporter 1) (4f2 light chain) (4f2 lc) (4f2lc) (cd98 light chain) (integral membrane protein e16) (hlat1). [swissprot;acc:q01650] Low confidence 7970.13 8357.56 387.43
    TTYH1 Ranked tweety homolog 1; tweety homolog. [refseq;acc:nm_020659] 205.156 198.715 6.441
    513 Divided no value myoglobin. [swissprot;acc:p02144] 205.157 1.03242
    AGPAT3 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] High confidence 7485.08 8543.66 1.14143
    DVL1 Ranked segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 218.596 204.344 1.06975
    GAD2 Squared glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Low confidence 51532.2 48514.9 1.06219
    PYCR2 Measured pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 8458.7 8868.63 1.04846
    RHOC Squared transforming protein rhoc (h9). [swissprot;acc:p08134] High confidence 19987.6 23960.7 1.19878
    RPL4 Rooted 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 51.5881 47.3127 1.09036
    SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Low confidence 70.5148 73.6785 1.04487
    Subtracted CCNE1 Squared g1/s-specific cyclin e1. [swissprot;acc:p24864] 49567.7 46799.3 2768.4
    CYGB Ranked cytoglobin (histoglobin) (hgb) (stellate cell activation-associated protein). [swissprot;acc:q8wwm9] 205.156 198.715 6.441
    DIRAS1 Measured small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] High confidence 6912.09 7734.41 822.32
    FLOT1 Rooted flotillin-1. [swissprot;acc:o75955] Low confidence 71.9847 75.2068 3.2221
    KRTAP9-8 Squared keratin associated protein 9.2. [refseq;acc:nm_031961] High confidence 31100.8 36090.1 4989.3
    LSM6 Ranked u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 227.483 212.994 14.489
    MAPK14 Rooted mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] 84.6378 89.8201 5.1823
    ZADH1 Measured zinc binding alcohol dehydrogenase, domain containing 1. [refseq;acc:nm_152444] Low confidence 8714.35 9101.44 387.09
    514 Divided AGPAT4 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] High confidence 7477 8532.02 1.1411
    DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Low confidence 7104.55 6776.72 1.04838
    DVL2 Ranked segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] High confidence 218.613 204.382 1.06963
    GAD1 Squared glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Low confidence 51532.2 48514.9 1.06219
    HBQ1 Ranked hemoglobin theta-1 chain. [swissprot;acc:p09105] 205.157 198.715 1.03242
    MICAL2 Rooted flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 70.5148 73.6785 1.04487
    TST Squared thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] High confidence 19987.6 23960.7 1.19878
    XAB2 Rooted xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 58.7805 64.0772 1.09011
    Subtracted no value Squared keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 31100.2 36086.5 4986.3
    AP3M1 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Low confidence 48405.1 45641.5 2763.6
    CHRNA4 Rooted neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] High confidence 84.6378 89.8201 5.1823
    DIRAS2 Measured di-ras2. [refseq;acc:nm_017594] 6912.08 7734.39 822.31
    FOXO3 Ranked forkhead box protein o3a (forkhead in rhabdomyosarcoma-like 1) (af6q21 protein). [swissprot;acc:o43524] Low confidence 205.156 198.715 6.441
    PAOX Measured peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 8843.04 9230.12 387.08
    PLRG1 Ranked pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] High confidence 222.893 208.523 14.37
    SOS2 Rooted son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Low confidence 72.3769 75.599 3.2221
    515 Divided no value Measured transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] High confidence 3890.53 4439.07 1.14099
    INPP4B Rooted inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Low confidence 70.5148 73.6785 1.04487
    LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] High confidence 56.3551 61.4322 1.09009
    MPST Squared 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 19987.6 23960.7 1.19878
    OXR1 oxidation resistance 1. [refseq;acc:nm_181354] Low confidence 47928.4 45127.4 1.06207
    PES1 Ranked pescadillo homolog 1. [swissprot;acc:o00541] High confidence 251.297 234.941 1.06962
    PYCR1 Measured pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Low confidence 8455.54 8864.47 1.04836
    TTYH1 Ranked tweety homolog 1; tweety homolog. [refseq;acc:nm_020659] 205.156 198.715 1.03241
    Subtracted no value Squared keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] High confidence 31100.2 36086.5 4986.3
    AKT1 Ranked rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 248.463 234.095 14.368
    APLP2 amyloid-like protein 2 precursor (amyloid protein homolog) (apph) (cdei-box binding protein) (cdebp). [swissprot;acc:q06481] Low confidence 205.156 198.715 6.441
    CHRNA3 Rooted neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] High confidence 84.6378 89.8201 5.1823
    ITGB1BP3 Measured muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Low confidence 8465.39 8851.43 386.04
    RRAD Squared gtp-binding protein rad (ras associated with diabetes) (rad1). [swissprot;acc:p55042] 48400.1 45637.3 2762.8
    SESN1 Rooted sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 71.9861 75.2076 3.2215
    XAB2 Measured xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] High confidence 5084.26 5904.1 819.84

    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/