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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 56924 to 56973 of 66312 in total
    Network Comparison Type  : Subtracted
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    2971 Rooted star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] STARD6 Low confidence 2.3192 70.8348 73.154
    2972 Measured acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] ACOX1 224.53 7989.61 8214.14
    steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285] NR5A1 High confidence 0 0 0
    Ranked proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] PSMB6 Low confidence 3.32 200.101 196.781
    steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285] NR5A1 High confidence 0 0 0
    Squared myelin gene expression factor 2. [refseq;acc:nm_016132] MYEF2 Low confidence 1543.2 39763.5 38220.3
    steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285] NR5A1 High confidence 0 0 0
    Rooted keratin associated protein 4.4. [refseq;acc:nm_032524] KRTAP4-4 Low confidence 2.3192 70.8348 73.154
    steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285] NR5A1 High confidence 0 0 0
    2973 Measured acyl-coa-binding protein (acbp) (diazepam binding inhibitor) (dbi) (endozepine) (ep). [swissprot;acc:p07108] DBI Low confidence 224.53 7989.61 8214.14
    fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062] ALDOB High confidence 0 0 0
    Ranked abl-philin 2. [refseq;acc:nm_032327] ZDHHC16 Low confidence 3.319 202.348 199.029
    fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062] ALDOB High confidence 0 0 0
    Squared
    t54 protein. [swissprot;acc:q92917] GPKOW Low confidence 1543.2 44633.1 43089.9
    Rooted fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062] ALDOB High confidence 0 0 0
    star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] STARD4 Low confidence 2.3192 70.8348 73.154
    2974 Measured cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750] CDK9 High confidence 0 0 0
    supervillin isoform 1; membrane-associated f-actin binding protein p205; archvillin. [refseq;acc:nm_003174] no value Low confidence 224.53 7989.61 8214.14
    Ranked cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750] CDK9 High confidence 0 0 0
    traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] TTRAP Low confidence 3.319 202.348 199.029
    Squared cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750] CDK9 High confidence 0 0 0
    hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] HAO2 Low confidence 1541.1 43743.6 42202.5
    Rooted cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750] CDK9 High confidence 0 0 0
    similar to peptidylprolyl isomerase a (cyclophilin a); cyclophilin-lc; cyclophilin homolog overexpressed in liver cancer; chromosome 1 amplified sequence 2. [refseq;acc:nm_178230] no value Low confidence 2.3191 70.8349 73.154
    2975 Measured potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121] KCTD3 High confidence 0 0 0
    solute carrier family 4, sodium bicarbonate cotransporter, member 7; sodium bicarbonate cotransporter 2; solute carrier family 4, sodium bicarbonate cotransporter, member 6. [refseq;acc:nm_003615] SLC4A7 Low confidence 224.53 7881.75 8106.28
    Ranked oxysterol binding protein-related protein 8 (osbp-related protein 8) (orp-8). [swissprot;acc:q9bzf1] OSBPL8 3.319 190.347 187.028
    potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121] KCTD3 High confidence 0 0 0
    Squared dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] no value Low confidence 1540.5 46114.5 44574
    potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121] KCTD3 High confidence 0 0 0
    Rooted
    star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] STARD5 Low confidence 2.3191 70.8349 73.154
    2976 Measured creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] CKMT2 224.44 8074.27 8298.71
    mo25 protein (cgi-66). [swissprot;acc:q9y376] CAB39 High confidence 0 0 0
    Ranked
    u3 snornp protein 4 homolog. [refseq;acc:nm_033416] IMP4 Low confidence 3.316 202.524 199.208
    Squared mo25 protein (cgi-66). [swissprot;acc:q9y376] CAB39 High confidence 0 0 0
    periodic tryptophan protein 1 homolog (keratinocyte protein ief ssp 9502). [swissprot;acc:q13610] PWP1 Low confidence 1539.5 45409.8 43870.3
    Rooted fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] AKTIP 2.3191 70.8451 73.1642
    mo25 protein (cgi-66). [swissprot;acc:q9y376] CAB39 High confidence 0 0 0
    2977 Measured cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] CYP27A1
    rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565] ARHGDIA Low confidence 224.42 7629.26 7853.68
    Ranked cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] CYP27A1 High confidence 0 0 0
    oxysterol binding protein-related protein 5 (osbp-related protein 5) (orp-5). [swissprot;acc:q9h0x9] OSBPL5 Low confidence 3.313 190.495 187.182
    Squared cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] CYP27A1 High confidence 0 0 0
    dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] TOP2B Low confidence 1539.3 46118.8 44579.5
    Rooted cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] CYP27A1 High confidence 0 0 0
    succinyl-coa:3-ketoacid-coenzyme a transferase, mitochondrial precursor (ec 2.8.3.5) (succinyl coa:3-oxoacid coa-transferase). [swissprot;acc:p55809] OXCT1 Low confidence 2.3191 70.8349 73.154
    2978 Measured creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] no value 224.41 8074.29 8298.7

    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/