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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Gene Rank Network Comparison Type Value Type description red Interaction Map green network_comparison Filtered
Results: HTML CSV LaTeX Showing element 551 to 600 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Value Type
description
red
green
network_comparison
69 Subtracted Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 178263 118639 59624
Rooted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 63.8686 47.2654 16.6032
70 Divided Measured amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 6475.5 10307.5 1.59177
Ranked guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 267.142 336.074 1.25804
Squared melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 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
Subtracted Measured 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] 17738.5 13995.7 3742.8
Ranked 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] 188.688 242.742 54.054
Squared gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 129597 73157.5 56439.5
Rooted myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 63.8686 47.2654 16.6032
71 Divided 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] 4556.78 2945.26 1.54716
Ranked guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] 267.144 336.073 1.25802
Squared melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 219048 129762 1.68808
Rooted doc-1 related protein (doc-1r). [swissprot;acc:o75956] 27.9136 37.2872 1.33581
Subtracted Measured 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] 17738.5 13995.7 3742.8
Ranked kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 265.686 319.651 53.965
Squared apg3p; pc3-96 protein. [refseq;acc:nm_022488] 129597 73157.5 56439.5
Rooted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 63.8686 47.2654 16.6032
72 Divided Measured uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 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
Squared melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 219048 129762 1.68808
Rooted neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 27.9136 37.2872 1.33581
Subtracted 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
Ranked potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 319.546 53.907
Squared 44050 protein. [refseq;acc:nm_178832] 148058 99628.4 48429.6
Rooted deltex 2. [refseq;acc:nm_020892] 27.634 43.9629 16.3289
73 Divided 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
Ranked junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 288 362 1.25694
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] 219048 129762 1.68808
Rooted neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 27.9136 37.2872 1.33581
Subtracted Measured serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 22268.8 18560.4 3708.4
Ranked 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] 265.632 319.531 53.899
Squared 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] 148058 99628.4 48429.6
Rooted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 27.7078 44.017 16.3092
74 Divided Measured 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] 4556.99 2945.8 1.54694
Ranked junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 288 362 1.25694
Squared trophinin. [swissprot;acc:q12816] 219048 129762 1.68808
Rooted neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 27.9136 37.2872 1.33581
Subtracted Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 20446.1 24136.4 3690.3
Ranked 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] 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
Rooted 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] 27.7254 44.0299 16.3045
75 Divided Measured 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] 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
Squared myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 110342 184298 1.67024
Rooted chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 27.9136 37.2872 1.33581
Subtracted Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 24136.4 3690.3
Ranked voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 254.693 202.668 52.025
Squared raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 117850 70566.8 47283.2
Rooted kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 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/