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 description Gene Network Comparison Type Value Type Interaction Map red network_comparison green Filtered
Results: HTML CSV LaTeX Showing element 551 to 600 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
red
network_comparison
green
69 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Subtracted Squared 178263 59624 118639
spermatogenesis associated 6. [refseq;acc:nm_019073] Divided Measured 6475.5 1.59177 10307.5
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 1.33581 37.2872
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Subtracted Squared 129597 56439.5 73157.5
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Divided Ranked 267.142 1.25804 336.074
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Squared 219048 1.68808 129762
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Subtracted Rooted 63.8686 16.6032 47.2654
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 3742.8 13995.7
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 54.054 242.742
71 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 129597 56439.5 73157.5
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided Rooted 27.9136 1.33581 37.2872
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Subtracted 63.8686 16.6032 47.2654
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Divided Ranked 267.144 1.25802 336.073
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Subtracted 265.686 53.965 319.651
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided Squared 219048 1.68808 129762
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 1.54716 2945.26
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 3742.8 13995.7
72 44050 protein. [refseq;acc:nm_178832] Squared 148058 48429.6 99628.4
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 3733.2 13977.7
deltex 2. [refseq;acc:nm_020892] Rooted 27.634 16.3289 43.9629
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Divided Ranked 267.144 1.25802 336.073
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared 219048 1.68808 129762
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Rooted 27.9136 1.33581 37.2872
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Subtracted Ranked 265.639 53.907 319.546
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Divided Measured 4556.79 1.54715 2945.28
73 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Subtracted Rooted 27.7078 16.3092 44.017
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Divided Ranked 288 1.25694 362
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 53.899 319.531
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 Squared 219048 1.68808 129762
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Rooted 27.9136 1.33581 37.2872
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 Squared 148058 48429.6 99628.4
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] Divided Measured 4556.83 1.54711 2945.38
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 22268.8 3708.4 18560.4
74 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared 117858 47287.9 70570.1
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured 20446.1 3690.3 24136.4
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Divided Ranked 288 1.25694 362
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Rooted 27.9136 1.33581 37.2872
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] Measured 4556.99 1.54694 2945.8
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 Ranked 189.07 53.383 242.453
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] Rooted 27.7254 16.3045 44.0299
trophinin. [swissprot;acc:q12816] Divided Squared 219048 1.68808 129762
75 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Rooted 27.9136 1.33581 37.2872
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Subtracted Measured 20446.1 3690.3 24136.4
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted 27.7254 16.3045 44.0299
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Divided Squared 110342 1.67024 184298
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] Measured 1920.75 1.5137 2907.43
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted Squared 117850 47283.2 70566.8
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] Divided Ranked 288 1.25694 362
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Subtracted 254.693 52.025 202.668

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/