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

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/