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

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/