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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 530 to 579 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
67 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Measured Divided 6475.5 10307.5 1.59177
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared Subtracted 144876 81136.5 63739.5
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Divided 267.14 336.075 1.25805
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared 219048 129762 1.68808
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 63.8686 47.2654 1.35128
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured Subtracted 17756.5 14007.3 3749.2
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] Ranked 187.458 243.677 56.219
68 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured Divided 6475.5 10307.5 1.59177
cyclin g2. [swissprot;acc:q16589] Subtracted 17738.6 13995.7 3742.9
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 139741 78454.6 61286.4
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 63.8686 47.2654 16.6032
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 1.35128
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked 267.139 336.075 1.25805
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 219048 129762 1.68808
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] Ranked Subtracted 187.462 243.673 56.211
69 cyclin g1 (cyclin g). [swissprot;acc:p51959] Measured 17738.5 13995.6 3742.9
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Rooted 63.8686 47.2654 16.6032
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked Divided 267.14 336.075 1.25805
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 219048 129762 1.68808
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] Ranked Subtracted 284.753 228.934 55.819
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Rooted Divided 27.9136 37.2872 1.33581
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared Subtracted 178263 118639 59624
spermatogenesis associated 6. [refseq;acc:nm_019073] Measured Divided 6475.5 10307.5 1.59177
70 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Rooted 27.9136 37.2872 1.33581
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared Subtracted 129597 73157.5 56439.5
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Ranked Divided 267.142 336.074 1.25804
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Squared 219048 129762 1.68808
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted Subtracted 63.8686 47.2654 16.6032
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Measured 17738.5 13995.7 3742.8
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] Ranked 188.688 242.742 54.054
71 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 129597 73157.5 56439.5
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Rooted Divided 27.9136 37.2872 1.33581
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Subtracted 63.8686 47.2654 16.6032
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Ranked 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] Subtracted 265.686 319.651 53.965
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared Divided 219048 129762 1.68808
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] Measured 4556.78 2945.26 1.54716
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Subtracted 17738.5 13995.7 3742.8
72 44050 protein. [refseq;acc:nm_178832] Squared 148058 99628.4 48429.6
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Measured 17710.9 13977.7 3733.2
deltex 2. [refseq;acc:nm_020892] Rooted 27.634 43.9629 16.3289
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Ranked Divided 267.144 336.073 1.25802
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared 219048 129762 1.68808
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Rooted 27.9136 37.2872 1.33581
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked Subtracted 265.639 319.546 53.907
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Measured Divided 4556.79 2945.28 1.54715
73 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted Subtracted 27.7078 44.017 16.3092
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Ranked 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] Subtracted 265.632 319.531 53.899

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/