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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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