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 Network Comparison Type Interaction Map Filtered Value Type red network_comparison green
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 77072 in total
Rank
description
Network Comparison Type
Interaction Map
Filtered
Value Type
red
network_comparison
green
32 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided High confidence 1 Measured 1834.73 2.04793 895.893
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 0 Rooted 0 9.43398 9.43398
implantation-associated protein. [refseq;acc:nm_032121] Low confidence 1 Measured 3278 1780.5 5058.5
importin 9. [refseq;acc:nm_018085] Divided High confidence 0 Ranked 13292.2 1.52929 8691.76
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Low confidence Rooted 9.84765 1.69589 5.80678
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 1 Squared 82347.8 1.33073 61881.5
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Subtracted High confidence Measured 23693.7 5430.7 18263
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided Low confidence 0 105.5 2.97183 35.5
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 3.41692 9.62112 0.355148
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 Rooted 145.551 1.1597 168.796
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted High confidence 0 Measured 859 801 58
myoglobin. [swissprot;acc:p02144] Divided Low confidence Ranked 11485.4 1.39162 15983.3
myosin regulatory light chain 2, nonsarcomeric (myosin rlc). [swissprot;acc:p19105] Subtracted Squared 54847.5 6799.3 48048.2
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided 1 Measured 36360.3 1.19275 43368.8
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Subtracted High confidence Squared 106226 85915 192141
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Divided 0 76.8994 16.8159 4.57302
pnas-129. [sptrembl;acc:q9bxv8] Subtracted Low confidence Ranked 11107.6 3734.8 14842.4
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Divided 1 273.188 1.17505 232.49
regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Subtracted 247.768 27.927 219.841
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] Divided High confidence 187.462 1.29985 243.673
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] Subtracted 0 Squared 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] Low confidence 1 Rooted 38.4152 10.7377 49.1529
ubiquitin protein ligase. [refseq;acc:nm_130466] Divided High confidence 0 24.0391 2.13529 11.258
33 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Subtracted Low confidence 1 Ranked 228.147 27.597 200.55
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] High confidence 0 Squared 29812 7010.7 36822.7
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Divided 76.8994 16.8159 4.57302
cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Subtracted Low confidence Ranked 11515 3648 7867
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1 Squared 77316.3 20794.2 56522.1
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] Divided Ranked 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] High confidence 0 Rooted 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] Low confidence Ranked 20324.1 1.37827 14746.1
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Subtracted High confidence 1 267.144 68.929 336.073
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided Measured 1835.3 2.04611 896.972
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Low confidence Squared 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] High confidence 0 Measured 12.6208 3.15402 39.8063
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Low confidence Rooted 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 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted High confidence 1 Measured 23693.7 5430.7 18263
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Divided Low confidence 0 105.5 2.97183 35.5
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Subtracted Squared 123984 6603 130587
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] High confidence Rooted 61.6393 9.359 70.9983
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Divided Ranked 13292.2 1.52929 8691.76
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Subtracted 1 Squared 106226 85915 192141
protein cgi-147. [swissprot;acc:q9y3e5] 0 Measured 8396.12 796.26 9192.38
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 1 Rooted 25.6987 17.8623 43.561
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Divided 26.0288 1.65937 43.1914
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence 76.5734 1.15738 88.6244
scribble. [refseq;acc:nm_015356] Subtracted 0 Measured 3697.8 547.36 4245.16
septin 6. [swissprot;acc:q14141] 1 13005.8 1767.9 14773.7

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/