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 Network Comparison Type green network_comparison Interaction Map red

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