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 description Filtered Value Type Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 77072 in total
Rank
Network Comparison Type
description
Filtered
Value Type
Interaction Map
red
network_comparison
green
32 Divided melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 0 Squared Low confidence 3.41692 9.62112 0.355148
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 Rooted 145.551 1.1597 168.796
myoglobin. [swissprot;acc:p02144] 0 Ranked 11485.4 1.39162 15983.3
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 Measured 36360.3 1.19275 43368.8
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 0 Squared High confidence 76.8994 16.8159 4.57302
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 1 Ranked Low confidence 273.188 1.17505 232.49
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] High confidence 187.462 1.29985 243.673
ubiquitin protein ligase. [refseq;acc:nm_130466] 0 Rooted 24.0391 2.13529 11.258
Subtracted cytohesin 4. [swissprot;acc:q9uia0] 1 Squared Low confidence 92262.9 20862.7 71400.2
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 0 Measured 2476.1 550.54 3026.64
fibrillin 3. [refseq;acc:nm_032447] Rooted 54.7341 6.8075 47.9266
gbp protein isoform a. [refseq;acc:nm_017870] 1 High confidence 23.9771 18.5002 42.4773
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Ranked 267.142 68.932 336.074
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 Rooted 0 9.43398 9.43398
implantation-associated protein. [refseq;acc:nm_032121] 1 Measured Low confidence 3278 1780.5 5058.5
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] High confidence 23693.7 5430.7 18263
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 859 801 58
myosin regulatory light chain 2, nonsarcomeric (myosin rlc). [swissprot;acc:p19105] Squared Low confidence 54847.5 6799.3 48048.2
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1 High confidence 106226 85915 192141
pnas-129. [sptrembl;acc:q9bxv8] 0 Ranked Low confidence 11107.6 3734.8 14842.4
regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] 1 247.768 27.927 219.841
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 0 Squared High confidence 19892.6 7328.6 27221.2
syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked 13884.4 5130.2 19014.6
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 Rooted Low confidence 38.4152 10.7377 49.1529
33 Divided beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 0 Squared High confidence 76.8994 16.8159 4.57302
dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] 1 Ranked Low confidence 210.241 1.17068 246.125
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 0 Rooted High confidence 12.3693 2.0801 25.7294
fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] Ranked Low confidence 20324.1 1.37827 14746.1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 1 Measured High confidence 1835.3 2.04611 896.972
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared Low confidence 82347.8 1.33073 61881.5
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 0 Measured High confidence 12.6208 3.15402 39.8063
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Rooted Low confidence 9.84765 1.69589 5.80678
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared 3.41692 9.62112 0.355148
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured 105.5 2.97183 35.5
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Ranked High confidence 13292.2 1.52929 8691.76
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 1 Rooted 26.0288 1.65937 43.1914
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence 76.5734 1.15738 88.6244
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 High confidence 188.688 1.28647 242.742
spermatogenesis associated 6. [refseq;acc:nm_019073] Squared 9924.76 2.53372 25146.6
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Measured Low confidence 36360.3 1.19275 43368.8
Subtracted ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Ranked 228.147 27.597 200.55
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 0 Squared High confidence 29812 7010.7 36822.7
cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Ranked Low confidence 11515 3648 7867
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1 Squared 77316.3 20794.2 56522.1
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Ranked High confidence 267.144 68.929 336.073
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Measured 23693.7 5430.7 18263
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 0 Squared Low confidence 123984 6603 130587
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Rooted High confidence 61.6393 9.359 70.9983
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 1 Squared 106226 85915 192141
protein cgi-147. [swissprot;acc:q9y3e5] 0 Measured 8396.12 796.26 9192.38

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/