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 1875 to 1924 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
469 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Squared 23531.7 28371.6 1.20568
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Measured 3831.17 4388.74 1.14554
470 block of proliferation 1. [swissprot;acc:q14137] 3796.24 4348.59 1.1455
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Ranked 248.152 267.226 1.07686
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Rooted 60.0148 65.6429 1.09378
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] Squared 10418.3 8641.84 1.20557
471 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Ranked 248.152 267.226 1.07686
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Measured 9649.61 11053.5 1.14549
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared 28188.7 33982.7 1.20554
vav-2 protein. [swissprot;acc:p52735] Rooted 66.088 72.2597 1.09339
472 gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared 28190.4 33984.1 1.20552
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Measured 9649.61 11053.5 1.14549
thymic stromal co-transporter. [refseq;acc:nm_033051] Ranked 248.152 267.226 1.07686
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Rooted 50.3767 46.0753 1.09336
473 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared 28190.4 33984.1 1.20552
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Ranked 225.661 209.651 1.07637
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Rooted 62.574 68.4128 1.09331
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Measured 9649.61 11053.5 1.14549
474 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Squared 28190.4 33984.1 1.20552
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Rooted 62.574 68.4128 1.09331
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Ranked 226.789 210.818 1.07576
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Measured 9649.61 11053.5 1.14549
475 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Rooted 62.574 68.4128 1.09331
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Measured 9649.61 11053.5 1.14549
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Squared 28192 33985.3 1.20549
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Ranked 226.727 210.816 1.07547
476 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Measured 9649.61 11053.5 1.14549
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Ranked 226.681 210.814 1.07527
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Rooted 62.574 68.4128 1.09331
vav proto-oncogene. [swissprot;acc:p15498] Squared 31223.8 37614.3 1.20467
477 inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Rooted 62.574 68.4128 1.09331
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Measured 9649.61 11053.5 1.14549
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Ranked 251.926 234.547 1.0741
vav-3 protein. [swissprot;acc:q9ukw4] Squared 31248.8 37623.4 1.204
478 histone h2b.c (h2b/c). [swissprot;acc:q99880] Rooted 50.6084 55.2961 1.09263
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared 16318.4 19645.8 1.2039
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Measured 9649.61 11053.5 1.14549
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Ranked 228.051 212.321 1.07409
479 histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Rooted 50.6084 55.2961 1.09263
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Ranked 228.051 212.321 1.07409
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Measured 9649.61 11053.5 1.14549
translation initiation factor if-2. [swissprot;acc:o60841] Squared 24031.6 28929.7 1.20382
480 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Rooted 50.6084 55.2961 1.09263
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Measured 9649.61 11053.5 1.14549
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Ranked 237.109 254.667 1.07405
phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] Squared 26874.6 32347.4 1.20364
481 histone h2b. [refseq;acc:nm_175055] Rooted 50.6084 55.2961 1.09263
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Measured 9649.61 11053.5 1.14549
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Ranked 237.109 254.667 1.07405
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared 16335.9 19660.7 1.20353

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/