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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 951 to 1000 of 77072 in total

Rank	Value Type	description	Network Comparison Type	Interaction Map	red	green	network_comparison	Filtered
30	Squared	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Subtracted	High confidence	23310.5	31089.6	7779.1	0
	Squared	trophinin. [swissprot;acc:q12816]			219048	129762	89286	1
	Rooted	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]			60.8022	79.5099	18.7077
		cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Divided	Low confidence	48.8781	56.7253	1.16055
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Subtracted	High confidence	0	9.43398	9.43398	0
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided	High confidence	26.0288	43.1914	1.65937	1
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Subtracted	Low confidence	44.4168	55.937	11.5202	1
		protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479]	Divided	Low confidence	13.0622	7.5	1.74163	0
		ptd016 protein. [refseq;acc:nm_016125]	Divided	High confidence	5.47723	12.5698	2.29492
		ptd016 protein. [refseq;acc:nm_016125]	Subtracted	Low confidence	5.47723	12.5698	7.09257
31	Measured	adenomatous polyposis coli like. [refseq;acc:nm_005883]	Subtracted	Low confidence	2544.19	3114.19	570
		dok-like protein. [refseq;acc:nm_024872]	Divided	High confidence	35	0.00001	3500000
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]		High confidence	1834.63	895.697	2.04827	1
		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]		Low confidence	105.5	35.5	2.97183	0
		melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Subtracted	High confidence	23693.7	18263	5430.7	1
		n33 protein. [swissprot;acc:q13454]		Low confidence	3278	5058.5	1780.5	1
		spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]		High confidence	1833	2637	804	0
		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Divided	Low confidence	36469.3	43503.3	1.19287	1
	Ranked	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Subtracted		142	170	28
		deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Divided		57.395	48.8186	1.17568
		guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Subtracted	High confidence	267.14	336.075	68.935
		hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	Divided	Low confidence	11485.6	15984.3	1.39168	0
		leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Divided	High confidence	8082.33	5266.67	1.53462
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Subtracted		11627	6248	5379
		serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	Divided		187.458	243.677	1.2999	1
		trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Subtracted	Low confidence	5575.71	9583.37	4007.66	0
	Squared	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Subtracted	High confidence	106226	192141	85915	1
		beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Divided	High confidence	9924.76	25146.6	2.53372
		cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Subtracted	Low confidence	92920.4	71796.4	21124
		fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Divided	High confidence	5.54059	103.726	18.7211	0
		fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Subtracted	High confidence	35446.2	27772	7674.2	0
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Divided	Low confidence	82347.8	61881.5	1.33073	1
		melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Divided		3.41692	0.355148	9.62112	0
		scribble. [refseq;acc:nm_015356]	Subtracted		19539.3	26377.5	6838.2	0
	Rooted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Divided		145.551	168.796	1.1597	1
		histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773]	Subtracted		67.7094	56.875	10.8344	1
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	High confidence	0	9.43398	9.43398	0
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Divided		12.1655	27.8029	2.28539	0
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted		40.0958	58.7986	18.7028	1
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Divided		26.0288	43.1914	1.65937	1
		segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Subtracted	Low confidence	58.6947	51.8401	6.8546	0
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Divided	Low confidence	7.3589	12.7411	1.73139
32	Measured	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Divided	High confidence	598	184	3.25
		dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	Subtracted	Low confidence	2476.1	3026.64	550.54
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Divided	High confidence	1834.73	895.893	2.04793	1
		implantation-associated protein. [refseq;acc:nm_032121]	Subtracted	Low confidence	3278	5058.5	1780.5
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Subtracted	High confidence	23693.7	18263	5430.7
		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Divided	Low confidence	105.5	35.5	2.97183	0
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Subtracted	High confidence	859	58	801	0
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Divided	Low confidence	36360.3	43368.8	1.19275	1

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/