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 red network_comparison green Filtered
Results: HTML CSV LaTeX Showing element 551 to 600 of 77072 in total
Rank
Value Type
description
Network Comparison Type
Interaction Map
red
network_comparison
green
Filtered
18 Measured mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted Low confidence 859 801 58 0
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Divided High confidence 677.5 2.75351 1865.5 1
Ranked 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 185.678 1.32082 245.247
early hematopoietic zinc finger. [refseq;acc:nm_015461] Low confidence 5850.23 1.52187 8903.28 0
elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] Subtracted 16116.4 4611.4 11505
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 6668.71 14178.1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 266.865 69.316 336.181 1
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 22286 1.68629 13216 0
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence 305.303 1.2352 247.169 1
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Subtracted 273.188 40.698 232.49
Squared adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided High confidence 439.709 841.001 0.52284 0
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Low confidence 2.31976 27.1495 0.0854438
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Subtracted High confidence 43393.5 13265.1 56658.6
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 122475 37292 159767 1
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] High confidence 219048 89286 129762
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided Low confidence 332411 1.42416 473408
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] High confidence 108.641 7.58176 823.69
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted Low confidence 9955.21 8769.19 18724.4 0
Rooted ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided High confidence 9.20014 6.52932 60.0707
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Low confidence 9.94987 2.28266 4.3589
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted High confidence 203.673 21.035 182.638 1
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Divided 21.4476 1.72261 36.9459
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted Low confidence 0 9.43398 9.43398 0
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Divided 44.4168 1.25937 55.937 1
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Subtracted High confidence 12.4097 12.4097 0 0
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Low confidence 32.2231 15.7049 47.928 1
19 Measured 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] Divided High confidence 305.45 11.6763 26.1599 0
Low confidence 3032.56 1.29112 3915.4 1
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted High confidence 24250 6085.1 18164.9
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 1593 1211 2804 0
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 4.3268 662
fos-related antigen 2. [swissprot;acc:p15408] Subtracted 3205.98 798.71 2407.27
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 15464.1 2108.6 17572.7 1
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Divided High confidence 677.5 2.75351 1865.5
Ranked alpha 2 globin. [refseq;acc:nm_000517] Subtracted Low confidence 11486.2 4500.9 15987.1 0
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided High confidence 185.678 1.32082 245.247 1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 266.865 69.313 336.178
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 40.211 228.509
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided High confidence 22286 1.68629 13216 0
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Subtracted 4475.84 6608.06 11083.9
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided Low confidence 3208.8 1.5182 4871.6
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 304.548 1.23387 246.824 1
Squared homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted 122475 37292 159767
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] High confidence 219048 89286 129762
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Divided 108.641 7.58176 823.69
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Subtracted 10489.8 12936.7 23426.5 0
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided Low confidence 6.25494 22.6931 141.944
serpin b12. [swissprot;acc:q96p63] High confidence 23.5744 813.196 0.0289898
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Subtracted Low confidence 124602 8591 133193
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Divided 332411 1.42416 473408 1

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/