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 Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
13 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided Low confidence 1 37.9984 29.1831 1.30207
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 288.754 212.554 1.3585
Subtracted Low confidence 255.046 202.362 52.684
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Divided 0 7435.56 12191.6 1.63963
14 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] Subtracted 1 286.396 238.476 47.92
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 13730.5 8257 5473.5
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Divided High confidence 1 56.6768 75.3531 1.32952
dystrophin. [swissprot;acc:p11532] 0 10232.5 18054.8 1.76446
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Subtracted 1 266.863 336.191 69.328
ptd016 protein. [refseq;acc:nm_016125] Divided Low confidence 0 18050 11234 1.60673
ubiquitin protein ligase. [refseq;acc:nm_130466] Subtracted High confidence 7523 15339.2 7816.2
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Divided Low confidence 1 37.9984 29.1831 1.30207
15 adenomatous polyposis coli like. [refseq;acc:nm_005883] 0 12074.1 7597.61 1.5892
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Subtracted 13109 18516 5407
cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] 1 286.347 238.454 47.893
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] High confidence 0 22422 14964 7458
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1 266.863 336.19 69.327
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Divided 56.7244 75.3948 1.32914
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 255.046 202.362 1.26035
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] High confidence 0 19403 11267 1.72211
16 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Low confidence 7395 11625 1.57201
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] High confidence 12170.7 20670.6 1.69839
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Subtracted Low confidence 1 284.798 237.743 47.055
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence 266.864 336.184 69.32
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided 56.7252 75.3954 1.32913
ptd016 protein. [refseq;acc:nm_016125] Subtracted 0 18050 11234 6816
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Low confidence 7435.56 12191.6 4756.04
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Divided 1 305.472 247.246 1.2355
17 bcl2-related ovarian killer. [refseq;acc:nm_032515] Subtracted 265.638 223.235 42.403
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Divided High confidence 56.7841 75.447 1.32866
ero1-like. [refseq;acc:nm_014584] Subtracted 0 13853 20536 6683
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 11543 6812 1.69451
Subtracted Low confidence 4731
gbp protein isoform a. [refseq;acc:nm_017870] Divided 1 305.399 247.213 1.23537
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Subtracted High confidence 266.864 336.182 69.318
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Divided Low confidence 0 8082.33 5266.67 1.53462
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 1 185.678 245.247 1.32082
early hematopoietic zinc finger. [refseq;acc:nm_015461] 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-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 0 22286 13216 1.68629
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence 1 305.303 247.169 1.2352
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Subtracted 273.188 232.49 40.698
19 alpha 2 globin. [refseq;acc:nm_000517] 0 11486.2 15987.1 4500.9
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 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-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided High confidence 0 22286 13216 1.68629
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Subtracted 4475.84 11083.9 6608.06

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/