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 1164 to 1213 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
73 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Measured Divided 0 65.2968 37.693 1.73233
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Squared Subtracted 10596.4 8278.87 2317.53
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Measured 1965.47 2389.69 424.22
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 1 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
74 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared 117858 70570.1 47287.9
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Ranked Divided 0 6742.5 8759.5 1.29915
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] Measured 501.151 859.34 1.71473
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Squared Subtracted 18585 20796.3 2211.3
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Ranked 14548.5 11915.2 2633.3
dok-like protein. [refseq;acc:nm_024872] Rooted 5.91608 0 5.91608
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Measured 14267.5 14688.8 421.3
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] Rooted Divided 5.01247 6.80523 1.35766
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured Subtracted 1 20446.1 24136.4 3690.3
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Ranked Divided 288 362 1.25694
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Rooted 27.9136 37.2872 1.33581
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Squared 0 0.092781 0.0318343 2.9145
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 1 4556.99 2945.8 1.54694
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] Ranked Subtracted 189.07 242.453 53.383
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 44.0299 16.3045
trophinin. [swissprot;acc:q12816] Squared Divided 219048 129762 1.68808
75 60s ribosomal protein l21. [swissprot;acc:p46778] Measured Subtracted 0 572 992.083 420.083
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Ranked 8158 5530.5 2627.5
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Rooted Divided 1 27.9136 37.2872 1.33581
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Subtracted 0 17.7787 23.6792 5.9005
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Measured 1 20446.1 24136.4 3690.3
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted 27.7254 44.0299 16.3045
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Squared Divided 0 6.13515 2.13609 2.87214
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 1 110342 184298 1.67024
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 2907.43 1.5137
nanos (fragment). [sptrembl;acc:q8wy41] Ranked 0 8782 11350 1.29242
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Measured 1586.07 925.298 1.71412
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Squared Subtracted 1 117850 70566.8 47283.2
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 0 4141.27 2000.69 2140.58
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] Rooted Divided 5.01247 6.80523 1.35766
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] Ranked 1 288 362 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
76 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Measured 0 598 184 414
cyclin g1 (cyclin g). [swissprot;acc:p51959] Squared 1 117718 70505.8 47212.2
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Rooted Divided 27.9136 37.2872 1.33581
db83 protein. [swissprot;acc:p57088] Ranked 288 362 1.25694
dead-box protein. [refseq;acc:nm_018665] Measured 0 313.667 183 1.71403
enigma protein; lim domain protein. [refseq;acc:nm_005451] Ranked Subtracted 14476.2 17069.5 2593.3
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Squared 7273.2 9308.93 2035.73
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Measured 1 20446.1 24136.4 3690.3
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Rooted 27.7254 44.0299 16.3045
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Squared Divided 110342 184298 1.67024
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 0 20.3193 57.5264 2.83112
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Rooted Subtracted 45.844 39.9449 5.8991
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] Measured Divided 1 4599.26 3058.57 1.50373

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/