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 Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 673 to 722 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    85 Measured fos-related antigen 2. [swissprot;acc:p15408] High confidence FOSL2 1.42395 4941.95 7037.11
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence DVL2 1.10843 7034.43 7797.14
    Ranked melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] High confidence no value 1.24949 88.2482 110.265
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Low confidence KCND2 1.08671 225.735 245.308
    Squared autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] High confidence ATG12 1.65709 67438.6 40697
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Low confidence no value 1.20712 60862.1 50419.2
    Rooted 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] High confidence NFYA 1.30362 46.7419 60.9337
    dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Low confidence DFFB 1.09453 61.1174 66.8946
    86 Measured protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence FOSB 1.42384 4942.49 7037.32
    vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Low confidence PTPRA 1.10773 7263.76 8046.29
    Ranked dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] DFFB 1.08645 233.922 215.309
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] High confidence MAGEA11 1.24949 88.2482 110.265
    Squared septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Low confidence SEPT7 1.2051 66860.1 80573.4
    transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] High confidence KRAS 1.64468 105500 64146.3
    Rooted 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] PPP2R1A 1.30146 63.6205 48.8838
    transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] Low confidence BACH1 1.09372 79.2778 86.7076
    87 Measured fos-related antigen 1 (fra-1). [swissprot;acc:p15407] High confidence FOSL1 1.42347 4944.3 7038.04
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Low confidence DVL3 1.10707 7054.1 7809.38
    Ranked melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] High confidence MAGEA2B 1.24949 88.2482 110.265
    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] Low confidence KCND3 1.08596 225.545 244.933
    Squared gaba-a receptor-associated protein. [sptrembl;acc:q9by60] no value 1.20496 60811 50467.3
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] High confidence SHOC2 1.64464 105482 64136.9
    Rooted 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] APBA1 1.30003 42.2825 54.9687
    nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] Low confidence NFE2L2 1.09372 79.2778 86.7076
    88 Measured potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence KCND2 1.42259 2411.93 1695.45
    serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Low confidence MAK 1.10399 9631.47 10633
    Ranked hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] High confidence no value 1.24949 88.2482 110.265
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Low confidence KCND1 1.0855 225.428 244.701
    Squared apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 1.2028 60759.9 50515.5
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] High confidence no value 1.64463 105482 64137.2
    Rooted presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] PSEN2 1.29795 37.3005 48.4141
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Low confidence BACH2 1.09372 79.2778 86.7076
    89 Measured cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] High confidence CTH 1.4217 2414.22 1698.12
    intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Low confidence ICK 1.10368 9623.55 10621.3
    Ranked melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] High confidence MAGEA6 1.24949 88.2482 110.265
    star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Low confidence STARD7 1.0853 228.743 210.764
    Squared protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] PPM1B 1.19821 69693.1 58164.5
    transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] High confidence HRAS 1.64462 105473 64132.3
    Rooted bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence BEST1 1.09199 187.345 204.579
    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] High confidence SKP1A 1.29795 37.3005 48.4141
    90 Measured 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] KCND3 1.4215 2414.77 1698.75
    vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552] Low confidence VASP 1.10341 12768 11571.4
    Ranked necdin. [swissprot;acc:q99608] High confidence NDN 1.24949 88.2482 110.265
    tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] Low confidence TAF2 1.08365 237.567 219.229
    Squared brca1 associated protein. [refseq;acc:nm_006768] BRAP 1.19626 83524.5 69821.2
    transforming protein n-ras. [swissprot;acc:p01111] High confidence no value 1.64461 105469 64130.2
    Rooted 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] FBXW7 1.29795 37.3005 48.4141
    vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence BEST4 1.09199 187.325 204.557
    91 Measured ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08] no value 1.10341 12768 11571.4
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] High confidence KCND1 1.42082 2416.53 1700.8

    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/