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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank Filtered description green Value Type Network Comparison Type red Interaction Map network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 77072 in total
Rank
Filtered
description
green
Value Type
Network Comparison Type
red
Interaction Map
network_comparison
18 0 camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] 19 Measured Divided 99 Low confidence 5.21053
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 56658.6 Squared Subtracted 43393.5 High confidence 13265.1
early hematopoietic zinc finger. [refseq;acc:nm_015461] 8903.28 Ranked Divided 5850.23 Low confidence 1.52187
elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] 11505 Subtracted 16116.4 4611.4
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 14178.1 7509.39 High confidence 6668.71
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 13216 Divided 22286 1.68629
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 9.43398 Rooted Subtracted 0 Low confidence 9.43398
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 58 Measured 859 801
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0 Rooted 12.4097 High confidence 12.4097
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 18724.4 Squared 9955.21 Low confidence 8769.19
1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 245.247 Ranked Divided 185.678 High confidence 1.32082
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 7251 Measured 5492.04 Low confidence 1.32027
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 182.638 Rooted Subtracted 203.673 High confidence 21.035
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 36.9459 Divided 21.4476 1.72261
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 336.181 Ranked Subtracted 266.865 69.316
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 17572.7 Measured 15464.1 Low confidence 2108.6
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 159767 Squared 122475 37292
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 247.169 Ranked Divided 305.303 1.2352
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 129762 Squared Subtracted 219048 High confidence 89286
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 18168.9 Measured 24255.7 6086.8
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 473408 Squared Divided 332411 Low confidence 1.42416
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 55.937 Rooted 44.4168 1.25937
232.49 Ranked Subtracted 273.188 40.698
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 823.69 Squared Divided 108.641 High confidence 7.58176
1865.5 Measured 677.5 2.75351
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 47.928 Rooted Subtracted 32.2231 Low confidence 15.7049
19 0 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] 26.1599 Measured Divided 305.45 High confidence 11.6763
alpha 2 globin. [refseq;acc:nm_000517] 15987.1 Ranked Subtracted 11486.2 Low confidence 4500.9
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 2804 Measured 1593 High confidence 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] 662 Divided 153 Low confidence 4.3268
fos-related antigen 2. [swissprot;acc:p15408] 2407.27 Subtracted 3205.98 798.71
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 9.43398 Rooted 0 9.43398
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 13216 Ranked Divided 22286 High confidence 1.68629
l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] 8.50775 Rooted 3.94084 Low confidence 2.15887
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 60.0707 9.20014 High confidence 6.52932
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 11083.9 Ranked Subtracted 4475.84 6608.06
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 4871.6 Divided 3208.8 Low confidence 1.5182
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 23426.5 Squared Subtracted 10489.8 High confidence 12936.7
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 11.7898 Rooted 23.8747 12.0849
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 141.944 Squared Divided 6.25494 Low confidence 22.6931
serpin b12. [swissprot;acc:q96p63] 0.0289898 23.5744 High confidence 813.196
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 133193 Subtracted 124602 Low confidence 8591
1 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] 3915.4 Measured Divided 3032.56 1.29112
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 18164.9 Subtracted 24250 High confidence 6085.1
cytohesin 4. [swissprot;acc:q9uia0] 182.638 Rooted 203.673 21.035
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 245.247 Ranked Divided 185.678 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 336.178 Subtracted 266.865 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] 228.509 188.298 Low confidence 40.211
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 17572.7 Measured 15464.1 2108.6
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 159767 Squared 122475 37292

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/