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 Value Type Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
69 Rooted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Subtracted 63.8686 47.2654 16.6032
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Divided 27.9136 37.2872 1.33581
70 Measured amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 6475.5 10307.5 1.59177
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] Subtracted 17738.5 13995.7 3742.8
Ranked guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 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] Subtracted 188.688 242.742 54.054
Squared gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 129597 73157.5 56439.5
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 219048 129762 1.68808
Rooted chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 27.9136 37.2872 1.33581
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Subtracted 63.8686 47.2654 16.6032
71 Measured 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] Divided 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
Ranked guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] 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
Squared apg3p; pc3-96 protein. [refseq;acc:nm_022488] 129597 73157.5 56439.5
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 219048 129762 1.68808
Rooted doc-1 related protein (doc-1r). [swissprot;acc:o75956] 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
72 Measured b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 17710.9 13977.7 3733.2
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Divided 4556.79 2945.28 1.54715
Ranked guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] 267.144 336.073 1.25802
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Subtracted 265.639 319.546 53.907
Squared 44050 protein. [refseq;acc:nm_178832] 148058 99628.4 48429.6
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Divided 219048 129762 1.68808
Rooted deltex 2. [refseq;acc:nm_020892] Subtracted 27.634 43.9629 16.3289
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Divided 27.9136 37.2872 1.33581
73 Measured 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] 4556.83 2945.38 1.54711
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 22268.8 18560.4 3708.4
Ranked junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 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
Squared melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Divided 219048 129762 1.68808
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Subtracted 148058 99628.4 48429.6
Rooted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 27.7078 44.017 16.3092
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Divided 27.9136 37.2872 1.33581
74 Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 20446.1 24136.4 3690.3
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] Divided 4556.99 2945.8 1.54694
Ranked junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 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] Subtracted 189.07 242.453 53.383
Squared a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 117858 70570.1 47287.9
trophinin. [swissprot;acc:q12816] Divided 219048 129762 1.68808
Rooted neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 27.9136 37.2872 1.33581
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Subtracted 27.7254 44.0299 16.3045
75 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 24136.4 3690.3
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Divided 1920.75 2907.43 1.5137
Ranked 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] 288 362 1.25694
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Subtracted 254.693 202.668 52.025
Squared myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Divided 110342 184298 1.67024
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted 117850 70566.8 47283.2
Rooted chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Divided 27.9136 37.2872 1.33581
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Subtracted 27.7254 44.0299 16.3045

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/