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.

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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 1980 to 2029 of 77072 in total

Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison
62	set and mynd domain containing protein 1. [sptrembl;acc:q8nb12]	Rooted	Divided	Low confidence	1	59.2532	66.0541	1.11478
	transcription factor jun-b. [swissprot;acc:p17275]	Measured	Subtracted			6613.42	7678.76	1065.34
	transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867]	Rooted				79.2778	86.7076	7.4298
	zinc finger protein basonuclin. [swissprot;acc:q01954]	Squared				105225	90141.3	15083.7
	zinc finger protein zfp6 (fragment). [sptrembl;acc:q92967]	Measured			0	2355.5	1972.28	383.22
63	60s ribosomal protein l37a. [swissprot;acc:p12751]	Ranked	Divided			12374.3	15783.5	1.27551
	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	Squared	Subtracted			53003.3	56866.2	3862.9
	core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156]	Squared	Divided		1	73677.6	57498.7	1.28138
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Rooted	Divided	High confidence	0	18.1049	12.6095	1.43581
	dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313]	Ranked	Subtracted	Low confidence		11636.2	14697.6	3061.4
	early hematopoietic zinc finger. [refseq;acc:nm_015461]	Rooted				57.5588	52.4931	5.0657
	gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335]	Squared			1	75927.4	61755.3	14172.1
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Ranked	Divided	High confidence		266.865	336.178	1.25973
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	Divided	Low confidence		15464.1	17572.7	1.13635
	jun dimerization protein. [refseq;acc:nm_130469]	Ranked	Subtracted	Low confidence		202.802	182.73	20.072
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Rooted	Divided	High confidence		43.4554	31.7576	1.36835
	laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]	Measured	Divided	Low confidence	0	154.208	75.6508	2.03842
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Rooted	Subtracted	High confidence	1	137.446	120.823	16.623
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Squared	Divided			219048	129762	1.68808
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Measured	Divided			4489.19	2765.82	1.6231
	nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236]	Rooted	Subtracted	Low confidence		79.2778	86.7076	7.4298
	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]	Ranked	Subtracted	High confidence		260.532	204.309	56.223
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Ranked	Divided		0	8519.83	11453	1.34428
	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	Measured	Subtracted			1442	977	465
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Squared	Divided			1.24091	0.365145	3.3984
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Rooted	Subtracted			37.9737	31.257	6.7167
	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Ranked	Divided	Low confidence	1	265.688	239.902	1.10749
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Measured	Subtracted	Low confidence	1	10618.8	11681.3	1062.5
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Squared	Subtracted	High confidence	0	99229.9	96418.4	2811.5
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Rooted	Divided	Low confidence	0	8.48528	12.2882	1.44818
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Squared	Subtracted	High confidence	1	189976	124480	65496
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Measured	Subtracted		1	6475.5	10307.5	3832
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Measured	Divided		0	31.1429	56.278	1.80709
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Ranked	Subtracted			18662.8	15627	3035.8
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Squared	Divided	Low confidence		44.2067	173.307	3.92038
	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Rooted	Divided		1	61.4851	68.1264	1.10801
	zinc finger protein 8 (zinc finger protein hf.18) (fragment). [swissprot;acc:p17098]	Measured	Subtracted		0	2355.41	1972.19	383.22
64	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Rooted	Divided	High confidence	1	63.8686	47.2654	1.35128
	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Squared	Subtracted	Low confidence	0	29525.8	33382.4	3856.6
	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Measured	Subtracted	High confidence	1	6475.5	10307.5	3832
	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Rooted	Divided	Low confidence	0	45.6289	66	1.44645
	b-lymphocyte activation-related protein. [sptrembl;acc:q96pn3]	Measured	Subtracted	Low confidence	0	2355.24	1972.04	383.2
	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]	Ranked		High confidence	1	260.532	204.309	56.223
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Squared			0	14470.6	11676.7	2793.9
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Squared			1	144940	81169.7	63770.3
	dna helicase homolog (fragment). [sptrembl;acc:q9y645]	Measured	Divided	Low confidence	0	48.2534	23.6984	2.03615
	early hematopoietic zinc finger. [refseq;acc:nm_015461]	Ranked	Subtracted		0	5850.23	8903.28	3053.05
	fos-related antigen 2. [swissprot;acc:p15408]	Ranked	Subtracted		1	202.793	182.961	19.832
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Measured	Divided	High confidence		4489.19	2765.82	1.6231
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Ranked	Divided	High confidence		266.868	336.159	1.25965

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/