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 description Filtered Gene green Value Type Interaction Map Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 501 to 550 of 38536 in total
Network Comparison Type  : Divided
Rank
description
Filtered
green
Value Type
Interaction Map
network_comparison
red
32 importin 9. [refseq;acc:nm_018085] 0 8691.76 Ranked High confidence 1.52929 13292.2
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 5.80678 Rooted Low confidence 1.69589 9.84765
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 1 61881.5 Squared 1.33073 82347.8
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 0 35.5 Measured 2.97183 105.5
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 0.355148 Squared 9.62112 3.41692
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 168.796 Rooted 1.1597 145.551
myoglobin. [swissprot;acc:p02144] 0 15983.3 Ranked 1.39162 11485.4
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 43368.8 Measured 1.19275 36360.3
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 0 4.57302 Squared High confidence 16.8159 76.8994
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 1 232.49 Ranked Low confidence 1.17505 273.188
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] 243.673 High confidence 1.29985 187.462
ubiquitin protein ligase. [refseq;acc:nm_130466] 0 11.258 Rooted 2.13529 24.0391
33 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 4.57302 Squared 16.8159 76.8994
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] 1 246.125 Ranked Low confidence 1.17068 210.241
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 25.7294 Rooted High confidence 2.0801 12.3693
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] 14746.1 Ranked Low confidence 1.37827 20324.1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 1 896.972 Measured High confidence 2.04611 1835.3
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 61881.5 Squared Low confidence 1.33073 82347.8
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 0 39.8063 Measured High confidence 3.15402 12.6208
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 5.80678 Rooted Low confidence 1.69589 9.84765
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 0.355148 Squared 9.62112 3.41692
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 35.5 Measured 2.97183 105.5
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 8691.76 Ranked High confidence 1.52929 13292.2
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 43.1914 Rooted 1.65937 26.0288
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 88.6244 Low confidence 1.15738 76.5734
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] 242.742 Ranked High confidence 1.28647 188.688
spermatogenesis associated 6. [refseq;acc:nm_019073] 25146.6 Squared 2.53372 9924.76
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] 43368.8 Measured Low confidence 1.19275 36360.3
34 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 25146.6 Squared High confidence 2.53372 9924.76
fibrillin 3. [refseq;acc:nm_032447] 0 7506.66 Ranked Low confidence 1.37724 5450.5
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 47 Measured High confidence 3.04255 143
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 1 24.3678 Rooted 1.65305 40.2812
907.546 Measured 2.02382 1836.71
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 0 0.697197 Squared 15.9968 0.0435834
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 5.80678 Rooted Low confidence 1.69589 9.84765
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 1 61881.5 Squared 1.33073 82347.8
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 0 0.355148 9.62112 3.41692
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 35.5 Measured 2.97183 105.5
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 17173.8 Ranked High confidence 1.52196 11284
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 11.7898 Rooted 2.02503 23.8747
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 6352.4 Measured Low confidence 1.1897 5339.5
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 133.876 Ranked 1.16197 155.56
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] 56.755 Rooted 1.15698 49.0544
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] 242.453 Ranked High confidence 1.28235 189.07
35 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 192141 Squared 1.80879 106226
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 0 647.816 12.7767 50.7031
1377 Measured 2.99674 459.5
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 11.7898 Rooted 2.02503 23.8747
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 1 39358.1 Measured Low confidence 1.18866 33111.4
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 24.3679 Rooted High confidence 1.65304 40.2812

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/