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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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

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/