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 673 to 722 of 14920 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    		description
    		Value Type
    		Filtered
    		red
    		green
    		network_comparison
    85 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Squared 1 67438.6 40697 1.65709
    bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 0 181.122 444.663 2.45505
    ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Rooted 1 46.7419 60.9337 1.30362
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 0 40.0375 29.9666 1.33607
    fos-related antigen 2. [swissprot;acc:p15408] Measured 1 4941.95 7037.11 1.42395
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Ranked 88.2482 110.265 1.24949
    rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] Measured 0 679.449 1106.88 1.62908
    transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Ranked 9688.47 12104.2 1.24934
    86 60s ribosomal protein l21. [swissprot;acc:p46778] Squared 146.619 359.589 2.45254
    alpha crystallin a chain. [swissprot;acc:p02489] Measured 55.3059 89.2447 1.61366
    high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] Ranked 5677.96 4546.87 1.24876
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Rooted 9.13761 12.1722 1.3321
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Ranked 1 88.2482 110.265 1.24949
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Measured 4942.49 7037.32 1.42384
    serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Rooted 63.6205 48.8838 1.30146
    transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Squared 105500 64146.3 1.64468
    87 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Rooted 42.2825 54.9687 1.30003
    dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] Ranked 0 5677.89 4547.43 1.24859
    dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Rooted 17.7787 23.6792 1.33189
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Measured 1 4944.3 7038.04 1.42347
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Squared 105482 64136.9 1.64464
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Ranked 88.2482 110.265 1.24949
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared 0 0.668702 1.63441 2.44415
    ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Measured 304.664 483.809 1.58801
    88 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Ranked 1 88.2482 110.265 1.24949
    high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 0 5677.86 4547.66 1.24852
    lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Rooted 3.4819 4.6274 1.32899
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Measured 1 2411.93 1695.45 1.42259
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted 37.3005 48.4141 1.29795
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Squared 105482 64137.2 1.64463
    thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Measured 0 304.664 483.809 1.58801
    transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Squared 13.9318 32.9409 2.36444
    89 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Measured 1 2414.22 1698.12 1.4217
    dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Rooted 0 39.9124 52.9528 1.32673
    importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Squared 21.5282 9.12314 2.35974
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked 1 88.2482 110.265 1.24949
    nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] 0 5677.58 4549.85 1.24786
    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] Rooted 1 37.3005 48.4141 1.29795
    suppressor of actin 1. [refseq;acc:nm_014016] Measured 0 23.6076 37.4843 1.58781
    transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Squared 1 105473 64132.3 1.64462
    90 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 0 67.8804 159.002 2.34238
    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] Rooted 1 37.3005 48.4141 1.29795
    high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] Ranked 0 5677.45 4550.87 1.24755
    importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] Rooted 24.6374 32.6803 1.32645
    metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Measured 34.6667 54.6667 1.57692
    necdin. [swissprot;acc:q99608] Ranked 1 88.2482 110.265 1.24949
    potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Measured 2414.77 1698.75 1.4215
    transforming protein n-ras. [swissprot;acc:p01111] Squared 105469 64130.2 1.64461
    91 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] Ranked 0 13841.2 11127.5 1.24387
    cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted 1 37.3005 48.4141 1.29795

    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/