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

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/