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 Gene Rank Value Type Network Comparison Type Interaction Map red description network_comparison green
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Filtered  : 0
Value Type  : Ranked
Rank
Network Comparison Type
Interaction Map
red
description
network_comparison
green
1 Divided High confidence 4294 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 3.70633 15915
Low confidence 5865 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 2.55362 14977
Subtracted High confidence 8906 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 12977 21883
Low confidence
2 Divided High confidence 5865 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 2.55362 14977
Low confidence 8906 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 2.45711 21883
Subtracted High confidence 4294 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 11621 15915
Low confidence 9607 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 11010 20617
3 Divided High confidence 4475.84 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 2.47638 11083.9
Low confidence 9607 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 2.14604 20617
Subtracted High confidence 21866 cab2. [refseq;acc:nm_033419] 10916 10950
Low confidence 9607 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] 11010 20617
4 Divided High confidence 8906 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 2.45711 21883
Low confidence 9607 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] 2.14604 20617
Subtracted High confidence 11525 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 10363 21888
Low confidence 5865 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 9112 14977
5 Divided High confidence 5510.5 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 2.17144 11965.7
Low confidence 10889.4 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 1.82499 19873
Subtracted High confidence 11525 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 10363 21888
Low confidence 22286 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 9070 13216
6 Divided High confidence 7523 ubiquitin protein ligase. [refseq;acc:nm_130466] 2.03897 15339.2
Low confidence 5575.71 trinucleotide repeat containing 15. [refseq;acc:nm_015575] 1.71877 9583.37
Subtracted High confidence 5865 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 9112 14977
Low confidence 22286 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 9070 13216
7 Divided High confidence 21866 cab2. [refseq;acc:nm_033419] 1.99689 10950
Low confidence 11543 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 1.69451 6812
Subtracted High confidence 22286 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 9070 13216
Low confidence homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
8 Divided High confidence 11525 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 1.89918 21888
Low confidence 22286 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 1.68629 13216
Subtracted High confidence homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 9070
Low confidence 10889.4 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 8983.6 19873
9 Divided High confidence 11525 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 1.89918 21888
Low confidence 22286 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 1.68629 13216
Subtracted High confidence homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 9070
Low confidence 22422 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] 7458 14964
10 Divided High confidence 7509.39 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 1.88805 14178.1
Low confidence 22286 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 1.68629 13216
Subtracted High confidence 20989 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 8510 12479
Low confidence 18050 ptd016 protein. [refseq;acc:nm_016125] 6816 11234
11 Divided High confidence 11627 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 1.86092 6248
Low confidence 13730.5 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 1.66289 8257
Subtracted High confidence 12170.7 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 8499.9 20670.6
Low confidence 14604.2 serpin b12. [swissprot;acc:q96p63] 6534.4 21138.6
12 Divided High confidence 9429.18 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 1.81023 5208.84
Low confidence 3190 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 1.65028 1933
Subtracted High confidence 19403 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] 8136 11267
Low confidence 14592 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 6521.7 21113.7
13 Divided High confidence 5210.5 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 1.77804 9264.5
Low confidence 7435.56 sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] 1.63963 12191.6

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/