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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank Network Comparison Type description Value Type Interaction Map green red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
Value Type
green
red
network_comparison
69 Subtracted 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 228.934 284.753 55.819
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 118639 178263 59624
70 Divided amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Measured 10307.5 6475.5 1.59177
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Rooted 37.2872 27.9136 1.33581
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Ranked 336.074 267.142 1.25804
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Squared 129762 219048 1.68808
Subtracted gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 73157.5 129597 56439.5
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 47.2654 63.8686 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 13995.7 17738.5 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 242.742 188.688 54.054
71 Divided doc-1 related protein (doc-1r). [swissprot;acc:o75956] Rooted 37.2872 27.9136 1.33581
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Ranked 336.073 267.144 1.25802
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared 129762 219048 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 2945.26 4556.78 1.54716
Subtracted apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 73157.5 129597 56439.5
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Rooted 47.2654 63.8686 16.6032
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Ranked 319.651 265.686 53.965
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] Measured 13995.7 17738.5 3742.8
72 Divided guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Ranked 336.073 267.144 1.25802
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared 129762 219048 1.68808
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Rooted 37.2872 27.9136 1.33581
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Measured 2945.28 4556.79 1.54715
Subtracted 44050 protein. [refseq;acc:nm_178832] Squared 99628.4 148058 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 13977.7 17710.9 3733.2
deltex 2. [refseq;acc:nm_020892] Rooted 43.9629 27.634 16.3289
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked 319.546 265.639 53.907
73 Divided junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 362 288 1.25694
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] Squared 129762 219048 1.68808
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Rooted 37.2872 27.9136 1.33581
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] Measured 2945.38 4556.83 1.54711
Subtracted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 44.017 27.7078 16.3092
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] Ranked 319.531 265.632 53.899
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] Squared 99628.4 148058 48429.6
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Measured 18560.4 22268.8 3708.4
74 Divided junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Ranked 362 288 1.25694
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Rooted 37.2872 27.9136 1.33581
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 2945.8 4556.99 1.54694
trophinin. [swissprot;acc:q12816] Squared 129762 219048 1.68808
Subtracted a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 70570.1 117858 47287.9
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured 24136.4 20446.1 3690.3
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 242.453 189.07 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 44.0299 27.7254 16.3045
75 Divided chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 37.2872 27.9136 1.33581
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Squared 184298 110342 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 2907.43 1920.75 1.5137
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 362 288 1.25694
Subtracted homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Measured 24136.4 20446.1 3690.3
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted 44.0299 27.7254 16.3045
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Squared 70566.8 117850 47283.2
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Ranked 202.668 254.693 52.025

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/