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 Value Type Rank Network Comparison Type red Interaction Map description green network_comparison

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Showing element 1 to 50 of 19268 in total

Filtered

: 0
Value Type

: Ranked

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