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 description green Filtered Value Type Interaction Map Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 38536 in total
Network Comparison Type  : Divided
Rank
description
green
Filtered
Value Type
Interaction Map
red
network_comparison
32 importin 9. [refseq;acc:nm_018085] 8691.76 0 Ranked High confidence 13292.2 1.52929
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 5.80678 Rooted Low confidence 9.84765 1.69589
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 61881.5 1 Squared 82347.8 1.33073
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 35.5 0 Measured 105.5 2.97183
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 0.355148 Squared 3.41692 9.62112
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 168.796 1 Rooted 145.551 1.1597
myoglobin. [swissprot;acc:p02144] 15983.3 0 Ranked 11485.4 1.39162
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 43368.8 1 Measured 36360.3 1.19275
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 4.57302 0 Squared High confidence 76.8994 16.8159
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 232.49 1 Ranked Low confidence 273.188 1.17505
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 187.462 1.29985
ubiquitin protein ligase. [refseq;acc:nm_130466] 11.258 0 Rooted 24.0391 2.13529
33 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 4.57302 Squared 76.8994 16.8159
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] 246.125 1 Ranked Low confidence 210.241 1.17068
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 25.7294 0 Rooted High confidence 12.3693 2.0801
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 20324.1 1.37827
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 896.972 1 Measured High confidence 1835.3 2.04611
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 61881.5 Squared Low confidence 82347.8 1.33073
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 39.8063 0 Measured High confidence 12.6208 3.15402
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 5.80678 Rooted Low confidence 9.84765 1.69589
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 0.355148 Squared 3.41692 9.62112
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 35.5 Measured 105.5 2.97183
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 8691.76 Ranked High confidence 13292.2 1.52929
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 43.1914 1 Rooted 26.0288 1.65937
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 88.6244 Low confidence 76.5734 1.15738
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 188.688 1.28647
spermatogenesis associated 6. [refseq;acc:nm_019073] 25146.6 Squared 9924.76 2.53372
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] 43368.8 Measured Low confidence 36360.3 1.19275
34 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 25146.6 Squared High confidence 9924.76 2.53372
fibrillin 3. [refseq;acc:nm_032447] 7506.66 0 Ranked Low confidence 5450.5 1.37724
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 47 Measured High confidence 143 3.04255
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 24.3678 1 Rooted 40.2812 1.65305
907.546 Measured 1836.71 2.02382
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 0.697197 0 Squared 0.0435834 15.9968
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 5.80678 Rooted Low confidence 9.84765 1.69589
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 61881.5 1 Squared 82347.8 1.33073
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 0.355148 0 3.41692 9.62112
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 35.5 Measured 105.5 2.97183
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 11284 1.52196
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 11.7898 Rooted 23.8747 2.02503
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 6352.4 1 Measured Low confidence 5339.5 1.1897
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 133.876 Ranked 155.56 1.16197
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] 56.755 Rooted 49.0544 1.15698
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 189.07 1.28235
35 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 192141 Squared 106226 1.80879
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 647.816 0 50.7031 12.7767
1377 Measured 459.5 2.99674
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 11.7898 Rooted 23.8747 2.02503
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 39358.1 1 Measured Low confidence 33111.4 1.18866
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 24.3679 Rooted High confidence 40.2812 1.65304

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/