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

Results: HTML CSV LaTeX

Showing element 8241 to 8290 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Value Type	red	network_comparison	green
2061	no value	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Squared	24225.6	1.08972	26399
	AP1S1	adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382]	Measured	5552.69	1.0564	5865.84
	CSDA	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]	Rooted	66.825	1.02631	68.5831
	TBC1D22B	tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]	Ranked	218.79	1.00834	216.981
2062	JPH4	adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843]	Measured	5552.7	1.0564	5865.85
	TBC1D22A	tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]	Ranked	218.79	1.00834	216.981
	YBX2	germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]	Rooted	66.825	1.02631	68.5831
	ZMYM6	zinc finger protein 258. [refseq;acc:nm_145310]	Squared	24225.6	1.08972	26399
2063	CNDP2	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4]	Rooted	65.2079	1.02628	66.9218
	ODC1	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	Ranked	207.638	1.00833	205.923
	SMARCC1	swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074]	Measured	5634.63	1.05635	5952.14
	ZMYM3	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]	Squared	24225.6	1.08972	26399
2064	AASS	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	Ranked	207.655	1.00833	205.939
	AP1B1	adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567]	Measured	5548.79	1.05632	5861.31
	PSMD10	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	Rooted	62.2279	1.02622	63.8594
	ZMYM4	zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]	Squared	24225.6	1.08972	26399
2065	ACTR2	actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]
	RPL35	60s ribosomal protein l35. [swissprot;acc:p42766]	Measured	3602.25	1.05631	3410.23
	SMARCC1	swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074]	Rooted	61.0898	1.02621	62.6908
	UBE2N	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	Ranked	214.328	1.00831	212.561
2066	COG3	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]	Squared	24225.6	1.08972	26399
	GNPNAT1	similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6]	Measured	5882.61	1.05622	6213.34
	PCNA	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	Ranked	229.102	1.00829	231.001
	RNF20	ring finger protein 20. [refseq;acc:nm_019592]	Rooted	59.5914	1.02621	61.1533
2067	no value	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Measured	3602.75	1.05616	3411.18
	ACTR3B	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]	Squared	24225.6	1.08972	26399
	ADSL	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566]	Ranked	193.226	1.00828	191.639
	COG6	conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7]	Rooted	66.6886	1.02621	68.4366
2068	ARPC1B	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Squared	24225.6	1.08972	26399
	FAIM	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	Ranked	220.8	1.0082	222.61
	MRPL2	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Measured	3602.75	1.05616	3411.17
	RNF40	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771]	Rooted	59.5914	1.02621	61.1533
2069	no value	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	Measured	4632.65	1.05613	4892.66
	MAP2K1	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750]	Ranked	217.555	1.0081	215.807
	NOB1	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	Rooted	55.9946	1.0262	57.4614
	ZMYM2	zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]	Squared	24225.6	1.08972	26399
2070	ACTR3	actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
	PBRM1	polybromo 1. [refseq;acc:nm_018165]	Rooted	61.089	1.02615	62.6862
	RACGAP1	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	Ranked	223.199	1.0081	225.008
	SFPQ	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]	Measured	10178.5	1.05607	9638.08
2071	ARPC3	arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]	Squared	24225.6	1.08972	26399
	KSR1	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	Ranked	217.555	1.0081	215.807
	MRPS26	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	Measured	6437.24	1.05592	6797.24
	SMARCA5	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]	Rooted	61.089	1.02615	62.6862
2072	ERH	enhancer of rudimentary homolog. [swissprot;acc:q14259]	Measured	6437.24	1.05592	6797.24
	MAP2K2	dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]	Ranked	217.555	1.0081	215.807
	NRD1	nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]	Squared	24225.6	1.08972	26399
	SMARCA4	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]	Rooted	61.089	1.02615	62.6862
2073	ARPC1A	actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]	Squared	24225.6	1.08972	26399
	PAPD5	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	Ranked	229.267	1.00806	227.433

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.