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 Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 125 to 174 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		green
    		network_comparison
    63 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] no value Divided 266.865 336.178 1.25973
    nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] NFYC Subtracted 260.532 204.309 56.223
    64 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] NFYA
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 Divided 266.868 336.159 1.25965
    65 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] GNAQ 267.136 336.077 1.25807
    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 Subtracted 187.457 243.678 56.221
    66 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] GNA11 Divided 267.136 336.077 1.25807
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D Subtracted 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
    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 187.458 243.677 56.219
    68 guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] GNAZ Divided 267.139 336.075 1.25805
    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 Subtracted 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
    70 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] GNAI2 Divided 267.142 336.074 1.25804
    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 Subtracted 188.688 242.742 54.054
    71 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] GNAI1 Divided 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
    72 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3 Divided 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
    73 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 Divided 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
    74 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 Divided 288 362 1.25694
    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 189.07 242.453 53.383
    75 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 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
    voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] CACNG3 Subtracted 254.693 202.668 52.025
    77 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] CACNG2 Divided 254.692 1.2567
    Subtracted 52.024
    78 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] CACNG4 254.691 52.023
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] CACNG8 Divided 254.693 1.2567
    79 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] CACNG3
    voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] CACNG5 Subtracted 254.614 202.646 51.968
    80 son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] SON 294.053 242.562 51.491
    voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] CACNG4 Divided 254.691 202.668 1.25669
    81 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 Subtracted 252.371 202.016 50.355
    voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] CACNG5 Divided 254.614 202.646 1.25645
    82 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] GNB5 267.636 335.359 1.25304
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] COQ7 Subtracted 252.329 202.004 50.325
    83 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 252.309 201.998 50.311
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] MAGED4 Divided 88.2482 110.265 1.24949
    84 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 Subtracted 252.296 201.995 50.301
    85 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] no value Divided 88.2482 110.265 1.24949
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A Subtracted 296.677 247.559 49.118
    86 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] DGCR14 335 286 49
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 Divided 88.2482 110.265 1.24949
    87 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] RBM15B Subtracted 249.663 298.263 48.6
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] MAGEA2B Divided 88.2482 110.265 1.24949

    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/