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 Filtered Rank green description Network Comparison Type Interaction Map Value Type network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
Filtered  : 0
Network Comparison Type  : Divided
Value Type  : Ranked
Rank
green
description
Interaction Map
network_comparison
red
1 14977 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 2.55362 5865
15915 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 3.70633 4294
2 14977 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 2.55362 5865
21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Low confidence 2.45711 8906
3 11083.9 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] High confidence 2.47638 4475.84
20617 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Low confidence 2.14604 9607
4 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 2.45711 8906
5 11965.7 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 2.17144 5510.5
19873 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 1.82499 10889.4
6 9583.37 trinucleotide repeat containing 15. [refseq;acc:nm_015575] 1.71877 5575.71
15339.2 ubiquitin protein ligase. [refseq;acc:nm_130466] High confidence 2.03897 7523
7 6812 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Low confidence 1.69451 11543
10950 cab2. [refseq;acc:nm_033419] High confidence 1.99689 21866
8 13216 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 1.68629 22286
21888 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] High confidence 1.89918 11525
9 13216 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 1.68629 22286
21888 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] High confidence 1.89918 11525
10 13216 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 1.68629 22286
14178.1 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] High confidence 1.88805 7509.39
11 6248 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 1.86092 11627
8257 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Low confidence 1.66289 13730.5
12 1933 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 1.65028 3190
5208.84 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] High confidence 1.81023 9429.18
13 9264.5 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 1.77804 5210.5
12191.6 sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Low confidence 1.63963 7435.56
14 11234 ptd016 protein. [refseq;acc:nm_016125] 1.60673 18050
18054.8 dystrophin. [swissprot;acc:p11532] High confidence 1.76446 10232.5
15 7597.61 adenomatous polyposis coli like. [refseq;acc:nm_005883] Low confidence 1.5892 12074.1
11267 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 1.72211 19403
16 11625 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Low confidence 1.57201 7395
20670.6 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] High confidence 1.69839 12170.7
17 5266.67 leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Low confidence 1.53462 8082.33
6812 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 1.69451 11543
18 8903.28 early hematopoietic zinc finger. [refseq;acc:nm_015461] Low confidence 1.52187 5850.23
13216 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence 1.68629 22286
19 4871.6 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 1.5182 3208.8
13216 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 1.68629 22286
20 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
14964 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] Low confidence 1.4984 22422
21 2582 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 1.49458 3859
10621.4 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] High confidence 1.68236 6313.38
22 7867 cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Low confidence 1.46371 11515
12479 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 1.68195 20989
23 9285.44 hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 1.67148 15520.4
21138.6 serpin b12. [swissprot;acc:q96p63] Low confidence 1.44743 14604.2
24 8257 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] High confidence 1.66289 13730.5
21113.7 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Low confidence 1.44694 14592
25 6909 nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 1.42278 9830
8257 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 1.66289 13730.5

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/