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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
18 camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Squared Divided Low confidence 0 2.31976 0.0854438 27.1495
Rooted 9.94987 4.3589 2.28266
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Squared Subtracted High confidence 43393.5 56658.6 13265.1
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Measured Divided Low confidence 1 5492.04 7251 1.32027
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted Subtracted High confidence 203.673 182.638 21.035
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Divided 21.4476 36.9459 1.72261
early hematopoietic zinc finger. [refseq;acc:nm_015461] Ranked Low confidence 0 5850.23 8903.28 1.52187
elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] Subtracted 16116.4 11505 4611.4
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] High confidence 7509.39 14178.1 6668.71
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1 266.865 336.181 69.316
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured Low confidence 15464.1 17572.7 2108.6
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Ranked Divided High confidence 0 22286 13216 1.68629
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Rooted Subtracted Low confidence 0 9.43398 9.43398
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared 1 122475 159767 37292
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Ranked Divided 305.303 247.169 1.2352
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared Subtracted High confidence 219048 129762 89286
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured 24255.7 18168.9 6086.8
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 0 859 58 801
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Squared Divided 1 332411 473408 1.42416
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked Subtracted 273.188 232.49 40.698
Rooted Divided 44.4168 55.937 1.25937
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Measured High confidence 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Rooted Subtracted 0 12.4097 0 12.4097
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Low confidence 1 32.2231 47.928 15.7049
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Squared 0 9955.21 18724.4 8769.19
19 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Measured Divided High confidence 305.45 26.1599 11.6763
Low confidence 1 3032.56 3915.4 1.29112
alpha 2 globin. [refseq;acc:nm_000517] Ranked Subtracted 0 11486.2 15987.1 4500.9
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured High confidence 1 24250 18164.9 6085.1
cytohesin 4. [swissprot;acc:q9uia0] Rooted 203.673 182.638 21.035
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Measured 0 1593 2804 1211
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Divided Low confidence 153 662 4.3268
fos-related antigen 2. [swissprot;acc:p15408] Subtracted 3205.98 2407.27 798.71
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked Divided High confidence 1 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 266.865 336.178 69.313
histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] Low confidence 188.298 228.509 40.211
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured 15464.1 17572.7 2108.6
Rooted 0 0 9.43398 9.43398
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared 1 122475 159767 37292
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Ranked Divided High confidence 0 22286 13216 1.68629
l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] Rooted Low confidence 3.94084 8.50775 2.15887
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 9.20014 60.0707 6.52932
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared Subtracted 1 219048 129762 89286
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Ranked Subtracted 0 4475.84 11083.9 6608.06
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided Low confidence 3208.8 4871.6 1.5182
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Squared Subtracted High confidence 10489.8 23426.5 12936.7
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Rooted 23.8747 11.7898 12.0849

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/