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 description green Interaction Map Network Comparison Type network_comparison red

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Rank	Value Type	description	green	Interaction Map	Network Comparison Type	network_comparison	red
1	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	High confidence	Subtracted	6325	85
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	Low confidence	Subtracted	6325	85
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	High confidence	Divided	36400000	364
			0.00001	Low confidence		36400000	364
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	High confidence		3.70633	4294
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	High confidence	Subtracted	12977	8906
			21883	Low confidence	Subtracted	12977	8906
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	Low confidence	Divided	2.55362	5865
	Squared	cab2. [refseq;acc:nm_033419]	7.16592	High confidence		716592	0.00001
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	Low confidence		187479	0.00001
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	High confidence	Subtracted	72283	232467
			160184	Low confidence		72283	232467
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	High confidence		50.8706	9.20014
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	Low confidence		50.8706	9.20014
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	High confidence	Divided	1907880	19.0788
			0.00001	Low confidence		1907880	19.0788
2	Measured	cab2. [refseq;acc:nm_033419]	174	High confidence		17400000	0.00001
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	Low confidence		8900000	0.00001
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	High confidence	Subtracted	6325	85
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	Low confidence		4196.8	23818.1
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	High confidence		11621	4294
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	Low confidence	Divided	2.45711	8906
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	High confidence	Divided	2.55362	5865
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	20617	Low confidence	Subtracted	11010	9607
	Squared	histone h4. [swissprot;acc:p02304]	345123	High confidence	Subtracted	71500	273623
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	Low confidence	Divided	187479	0.00001
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	High confidence	Divided	561325	5.61325
		transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	386144	Low confidence	Subtracted	28560	414704
	Rooted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	9.43398	Low confidence	Divided	943398	0.00001
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	60.0707	High confidence	Subtracted	50.8706	9.20014
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	7.61577	Low confidence	Subtracted	21.6929	29.3087
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	High confidence	Divided	1240970	12.4097
3	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	Low confidence	Divided	8900000	0.00001
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	High confidence	Subtracted	4196.8	23818.1
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7500.75	Low confidence	Subtracted	2393.82	5106.93
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	High confidence	Divided	10900000	0.00001
	Ranked	cab2. [refseq;acc:nm_033419]	10950	High confidence	Subtracted	10916	21866
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	20617	Low confidence	Divided	2.14604	9607
		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	20617	Low confidence	Subtracted	11010	9607
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	High confidence	Divided	2.47638	4475.84
	Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	170628	High confidence	Subtracted	35348	135280
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.87479	Low confidence	Divided	187479	0.00001
		rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	197937	Low confidence	Subtracted	23051	220988
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	High confidence	Divided	561325	5.61325
	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	6.85565	High confidence	Subtracted	30.0631	36.9188
		anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	66	Low confidence	Subtracted	20.3711	45.6289
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	9.43398	Low confidence	Divided	943398	0.00001
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	High confidence	Divided	1240970	12.4097
4	Measured	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	4356	Low confidence	Subtracted	2274	2082
4	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	Low confidence	Divided	8900000	0.00001

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/