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

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 275 to 324 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Divided	2755.15	2094.3	1.31555
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Subtracted	15182.5	13277.9	1904.6
139	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]		12780.7	10876.4	1904.3
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Divided	2759.61	2099.49	1.31442
140	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Subtracted	2597.5	698.5	1899
	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]	Divided	2760.28	2100.27	1.31425
141	hbs1-like. [refseq;acc:nm_006620]	Subtracted	2597.5	698.5	1899
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Divided	4405.4	5782.08	1.3125
142	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]		9276.47	7090.37	1.30832
	transcription factor jun-d. [swissprot;acc:p17535]	Subtracted	5638.2	7523.39	1885.19
143	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Divided	9275.1	7089.65	1.30826
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Subtracted	15427.2	13572.8	1854.4
144	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]		4133.47	5945.32	1811.85
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Divided	3349.9	4362.61	1.30231
145	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Subtracted	4136.36	5943.56	1807.2
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Divided	16771.5	12889.1	1.30122
146	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]		11068	8508.5	1.30082
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Subtracted	2671	871	1800
147	protein x 0004. [refseq;acc:nm_016301]
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Divided	11068	8508.5	1.30082
148	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
	symplekin. [swissprot;acc:q92797]	Subtracted	15213.4	13418.1	1795.3
149	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Divided	11068	8508.5	1.30082
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Subtracted	11736.6	13531.9	1795.3
150	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Divided	11068	8508.5	1.30082
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Subtracted	4172.91	5954.48	1781.57
151	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]		14830.5	13050.3	1780.2
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Divided	4578.09	5939.91	1.29746
152	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	Subtracted	5136.78	6895.98	1759.2
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Divided	23693.7	18263	1.29736
153	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Subtracted	9035	7279.6	1755.4
154	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Divided	23693.7	18263	1.29736
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Subtracted	9035	7279.6	1755.4
155	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Divided	23693.7	18263	1.29736
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Subtracted	9035	7279.6	1755.4
156	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Divided	23693.7	18263	1.29736
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Subtracted	9035	7279.6	1755.4
157	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Divided	23693.7	18263	1.29736
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Subtracted	9035	7279.6	1755.4
158	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Divided	23693.7	18263	1.29736
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Subtracted	9035	7279.6	1755.4
159	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
	necdin. [swissprot;acc:q99608]	Divided	23693.7	18263	1.29736
160	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Subtracted	9035	7279.6	1755.4
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Divided	23693.7	18263	1.29736
161	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Subtracted	9035	7279.6	1755.4
162	high-mobility group 20a. [refseq;acc:nm_018200]		5140.14	6893.53	1753.39
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Divided	23693.7	18263	1.29736

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.