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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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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 1394 to 1443 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
88	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Ranked	Divided	1	88.2482	110.265	1.24949
	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	Ranked		0	5677.86	4547.66	1.24852
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Rooted			3.4819	4.6274	1.32899
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	Subtracted		364	0	364
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Ranked	Subtracted		12787.8	10454.7	2333.1
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Measured	Divided	1	2411.93	1695.45	1.42259
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Rooted			37.3005	48.4141	1.29795
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Squared			105482	64137.2	1.64463
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Ranked	Subtracted		249.663	298.263	48.6
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Squared	Subtracted	0	7073.9	8609.96	1536.06
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Measured	Divided	0	304.664	483.809	1.58801
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Measured	Subtracted	1	16074	12888.4	3185.6
	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	Squared	Divided	0	13.9318	32.9409	2.36444
	tubby protein homolog. [swissprot;acc:p50607]	Rooted	Subtracted	0	39.7788	45.0452	5.2664
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared		1	98517.9	56927.2	41590.7
89	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Ranked		0	12049	14370.7	2321.7
	block 23. [sptrembl;acc:q8nhw5]	Squared		0	14555.7	16084.7	1529
	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Measured	Divided	1	2414.22	1698.12	1.4217
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Rooted	Divided	0	39.9124	52.9528	1.32673
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Rooted	Subtracted	1	40.3372	24.3043	16.0329
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Measured	Subtracted	0	4088	4451	363
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Squared	Divided	0	21.5282	9.12314	2.35974
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Measured	Subtracted	1	16071.6	12886.8	3184.8
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Ranked	Divided	1	88.2482	110.265	1.24949
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Ranked	Divided	0	5677.58	4549.85	1.24786
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	Rooted	Subtracted	0	14.1508	8.89106	5.25974
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Ranked	Subtracted	1	249.663	298.263	48.6
	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]	Rooted	Divided	1	37.3005	48.4141	1.29795
	suppressor of actin 1. [refseq;acc:nm_014016]	Measured		0	23.6076	37.4843	1.58781
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	Squared		1	105473	64132.3	1.64462
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Squared	Subtracted	1	105500	64146.3	41353.7
90	60s ribosomal protein l18a. [swissprot;acc:q02543]	Ranked		0	12738.7	10437.1	2301.6
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Rooted			18.7392	13.5207	5.2185
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Measured			2145.97	1784.22	361.75
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Squared	Divided		67.8804	159.002	2.34238
	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	Squared	Subtracted		3338.97	4832.12	1493.15
	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	Rooted	Divided	1	37.3005	48.4141	1.29795
	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	Ranked		0	5677.45	4550.87	1.24755
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Rooted		0	24.6374	32.6803	1.32645
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Squared	Subtracted	1	105482	64136.9	41345.1
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Measured	Divided	0	34.6667	54.6667	1.57692
	necdin. [swissprot;acc:q99608]	Ranked		1	88.2482	110.265	1.24949
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	Measured			2414.77	1698.75	1.4215
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Measured	Subtracted		16071.6	12886.8	3184.8
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	Ranked			249.663	298.263	48.6
	transcription factor jun-d. [swissprot;acc:p17535]	Rooted			63.636	79.6225	15.9865
	transforming protein n-ras. [swissprot;acc:p01111]	Squared	Divided		105469	64130.2	1.64461
91	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Squared	Subtracted	0	4734.34	6172.1	1437.76
	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	Measured	Subtracted		501.151	859.34	358.189
		Ranked	Divided		13841.2	11127.5	1.24387

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/