MK5 Microarray Data

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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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	Hugo	Value Type	Network Comparison Type	description	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 2841 to 2890 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	Value Type	Network Comparison Type	description	red	green	network_comparison
356	no value	Ranked	Divided	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	243.24	266.796	1.09684
	LSM8	Rooted	Subtracted	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	56.031	62.8281	6.7971
	PRKAG3	Squared		5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]	34129.6	40434.5	6304.9
	SF3B2	Rooted	Divided	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]	58.0752	64.23	1.10598
	SH3GL3	Squared		sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	35247.5	43820.5	1.24322
	SNRPA1	Measured	Subtracted	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	4914.27	5907.12	992.85
	TCP1		Divided	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	11004.2	12944.2	1.1763
	VPS24	Ranked	Subtracted	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	94	114	20
357	no value		Divided	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12	266.661	1.09683
		Rooted	Subtracted	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	46.3291	53.1063	6.7772
	CHMP4A	Ranked		protein hspc134 (protein cda04). [swissprot;acc:q9by43]	94	114	20
	DVL1	Measured		segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	4977.09	5966.44	989.35
	GRB2	Rooted	Divided	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	61.2684	67.755	1.10587
	IMMP2L	Measured		imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	5061.11	5950.22	1.17567
	PPP2R2D	Squared		uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	9811.86	7908.29	1.24071
	PRKAB1		Subtracted	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	34129.6	40434.5	6304.9
358	no value	Measured	Divided	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	5061.11	5950.22	1.17567
		Squared		serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	9811.73	7908.13	1.24071
	DVL2	Measured	Subtracted	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	4977.8	5966.14	988.34
	NEK2	Rooted	Divided	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955]	61.2684	67.755	1.10587
	NFYB		Subtracted	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	51.6736	58.4422	6.7686
	PRKAG2	Squared		5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	34129.6	40434.5	6304.9
	RAB37	Ranked		ras-related protein rab-37. [swissprot;acc:q96ax2]	240.287	260.193	19.906
	RPL10L		Divided	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	243.12	266.662	1.09683
359	CDK3	Measured		cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	12798.9	10887.2	1.17559
	NDUFS4		Subtracted	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	1920.75	2907.43	986.68
	PES1	Rooted	Divided	pescadillo homolog 1. [swissprot;acc:o00541]	49.2488	54.4603	1.10582
	PPP2R2B	Squared		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]	9812.34	7908.87	1.24068
	PRKAA1		Subtracted	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	34129.4	40434.2	6304.8
	RAB26	Ranked		ras-related protein rab-26. [swissprot;acc:q9ulw5]	240.287	260.193	19.906
	RPL4		Divided	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	239.277	262.434	1.09678
	SART1	Rooted	Subtracted	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	57.6823	64.4212	6.7389
360	CCNB2	Measured	Divided	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	12796.8	10886	1.17553
	DDX24	Rooted	Subtracted	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	46.901	53.624	6.723
	GNL3		Divided	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	49.3771	54.5905	1.10558
	LSM8	Measured	Subtracted	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	4590.18	5575.52	985.34
	POLR2C	Ranked		dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]	240.287	260.193	19.906
	PPP2R2C	Squared	Divided	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	9814.47	7911.48	1.24054
	SEC61G	Ranked		protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	243.072	266.559	1.09663
	VAV2	Squared	Subtracted	vav-2 protein. [swissprot;acc:p52735]	31377.3	37670.1	6292.8
361	CAPN2	Rooted		calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	46.8525	53.5324	6.6799
	CBL	Measured		cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	6875.08	7858.38	983.3
	CDK2		Divided	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	12787.6	10880.5	1.17528
	KATNA1	Ranked	Subtracted	katanin p60 subunit a 1. [refseq;acc:nm_007044]	232.431	252.238	19.807
	MRPL17		Divided	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	242.83	266.248	1.09644
	RPS4Y2	Rooted		40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	50.7801	45.9472	1.10518
	SFPQ	Squared		splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246]	70694.1	56989.9	1.24047
	TPT1		Subtracted	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	42363.8	36083.8	6280
362	no value			nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	34071.5	40336.5	6265
		Rooted	Divided	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	50.7803	45.9477	1.10518

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
- Hugo is the HGNC identifier if it exists
- 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.