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.

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.

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

Results: HTML CSV LaTeX

Showing element 4708 to 4757 of 66312 in total

Filtered  : 1

Rank	description	Value Type	Network Comparison Type	Interaction Map	red	green	network_comparison
295	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Measured	Subtracted	High confidence	5720.25	4577.5	1142.75
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	Ranked			219.421	196.978	22.443
	iroquois-class homeodomain protein irx-2 (iroquois homeobox protein 2) (fragment). [swissprot;acc:q9bzi1]	Measured		Low confidence	8966.8	9445.26	478.46
	lbp-9. [refseq;acc:nm_014553]	Rooted			65.5843	69.3703	3.786
	mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940]	Squared			49043.9	45220	3823.9
	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Ranked	Divided	High confidence	223.273	202.423	1.103
	myocyte-specific enhancer factor 2d. [swissprot;acc:q14814]			Low confidence	218.713	209.709	1.04294
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	Squared	Subtracted	High confidence	28896.2	36767	7870.8
	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	Rooted			66.1064	74.1074	8.001
	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	Measured	Divided		13261.9	11017.8	1.20368
	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	Rooted			59.029	65.9421	1.11711
	tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [swissprot;acc:q9h2k2]			Low confidence	66.6351	70.2333	1.054
	ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441]	Squared			57470.4	53017.7	1.08399
296	diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910]	Measured	Subtracted		6519.03	6997.26	478.23
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Ranked			199.66	191.203	8.457
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Rooted	Divided	High confidence	63.0663	56.4667	1.11688
	fibulin-1 precursor. [swissprot;acc:p23142]	Squared		Low confidence	51225	47264.3	1.0838
	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]		Subtracted	High confidence	28896.4	36766.8	7870.4
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Ranked			219.421	196.978	22.443
	jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504]		Divided	Low confidence	218.714	209.709	1.04294
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]			High confidence	241.282	266.12	1.10294
	neuronal guanine nucleotide exchange factor. [refseq;acc:nm_019850]	Squared	Subtracted	Low confidence	48964.5	45143	3821.5
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Measured		High confidence	3620.77	4763.34	1142.57
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	Rooted			66.1064	74.1074	8.001
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]		Divided	Low confidence	84.7416	89.3094	1.0539
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	Measured		High confidence	4911.81	5909.18	1.20306
	tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066]			Low confidence	8417.28	8911.22	1.05868
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Rooted	Subtracted		65.5878	69.373	3.7852
	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	Squared	Divided	High confidence	28878.8	36783.5	1.27372
297	60s ribosomal protein l7. [swissprot;acc:p18124]	Ranked			235.727	259.984	1.1029
	alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745]	Rooted	Subtracted	Low confidence	65.5904	69.3751	3.7847
	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	Squared		High confidence	28900.8	36762.6	7861.8
	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Measured			3620.77	4763.34	1142.57
	diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760]			Low confidence	6519.03	6997.26	478.23
	dual specificity protein kinase ttk (ec 2.7.1.-) (pyt). [swissprot;acc:p33981]	Squared			47648.2	43829.4	3818.8
	fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020]	Measured	Divided		8414.05	8907.06	1.05859
	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]			High confidence	4911.81	5909.18	1.20306
	large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5]	Ranked	Subtracted	Low confidence	205.154	196.72	8.434
	mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796]	Squared	Divided		48958.6	45174.5	1.08377
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Ranked	Subtracted	High confidence	219.421	196.978	22.443
	myocyte-specific enhancer factor 2c. [swissprot;acc:q06413]		Divided	Low confidence	218.714	209.709	1.04294
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Rooted			61.3254	58.1927	1.05383
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Squared		High confidence	14247.4	18142.1	1.27336
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	Rooted			63.0663	56.4667	1.11688
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]		Subtracted		66.1064	74.1073	8.0009
298	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109]	Measured			8268.19	9405.85	1137.66
	bet3 homolog. [swissprot;acc:o43617]	Rooted	Divided	Low confidence	75.2506	79.2999	1.05381
	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]	Ranked		High confidence	268.632	243.588	1.10281
	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	Squared	Subtracted	Low confidence	50189.4	46383.9	3805.5
	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Measured	Divided		8708.47	9218.39	1.05855

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.