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 Hugo Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 258 to 307 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    65 protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB Subtracted Low confidence 202.792 182.974 19.818
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] no value High confidence 187.457 243.678 56.221
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Divided Low confidence 202.728 183.388 1.10546
    66 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 Subtracted 202.79 183.017 19.773
    guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] GNA11 Divided High confidence 267.136 336.077 1.25807
    mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] MTUS1 Low confidence 221.902 200.783 1.10518
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D Subtracted High confidence 187.458 243.678 56.22
    67 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] GNAT2 Divided 267.14 336.075 1.25805
    putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] AHCYL1 Subtracted Low confidence 195.817 215.516 19.699
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] UBR4 Divided 165.535 149.799 1.10505
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] PPP2R2B Subtracted High confidence 187.458 243.677 56.219
    68 60s ribosomal protein l37a. [swissprot;acc:p12751] no value Divided Low confidence 239.692 217.005 1.10455
    guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] GNAZ High confidence 267.139 336.075 1.25805
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] KCND2 Subtracted Low confidence 225.735 245.308 19.573
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] PPP2R2C High confidence 187.462 243.673 56.211
    69 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] GNAT1 Divided 267.14 336.075 1.25805
    nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] NDUFA12 Subtracted 284.753 228.934 55.819
    putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] no value Low confidence 195.851 215.424 19.573
    testis-specific protein tex28. [swissprot;acc:o15482] TEX28P2 Divided 259.517 235.017 1.10425
    70 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] GOSR2
    guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] GNAI2 High confidence 267.142 336.074 1.25804
    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 Subtracted Low confidence 225.545 244.933 19.388
    serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] PPP2R1B High confidence 188.688 242.742 54.054
    71 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] no value Divided Low confidence 230.944 209.149 1.10421
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] GNAI1 High confidence 267.144 336.073 1.25802
    kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] KCNIP1 Subtracted 265.686 319.651 53.965
    transcription factor jun-d. [swissprot;acc:p17535] JUND Low confidence 202.709 183.361 19.348
    72 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3 Divided High confidence 267.144 336.073 1.25802
    potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] KCNIP4 Subtracted 265.639 319.546 53.907
    set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] SMYD2 Divided Low confidence 230.944 209.149 1.10421
    transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] TFDP2 Subtracted 227.623 208.281 19.342
    73 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 Divided High confidence 288 362 1.25694
    kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] KCNIP2 Subtracted 265.632 319.531 53.899
    set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] SMYD1 Divided Low confidence 230.944 209.149 1.10421
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Subtracted 202.728 183.388 19.34
    74 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 Divided High confidence 288 362 1.25694
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] KCND1 Subtracted Low confidence 225.428 244.701 19.273
    putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] AHCYL1 Divided 195.817 215.516 1.1006
    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 Subtracted High confidence 189.07 242.453 53.383
    75 nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS Divided Low confidence 249.709 226.944 1.10031
    rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 Subtracted 221.194 202.005 19.189
    sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] SMPD2 Divided High confidence 288 362 1.25694
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] CACNG8 Subtracted 254.693 202.668 52.025
    76 db83 protein. [swissprot;acc:p57088] TMEM33 Divided 288 362 1.25694
    diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] DGKH Subtracted Low confidence 226.981 208.077 18.904
    nipsnap1 protein. [swissprot;acc:q9bpw8] NIPSNAP1 Divided 249.584 226.86 1.10017
    voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] CACNG3 Subtracted High confidence 254.693 202.668 52.025
    77 diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] DGKD Low confidence 226.981 208.077 18.904
    putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] no value Divided 195.851 215.424 1.09994
    voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] CACNG2 High confidence 254.692 202.668 1.2567

    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/