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

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Showing element 3308 to 3357 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
207	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Rooted	Divided	0	13.6748	12	1.13957
	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	Squared		1	70525.9	52678.7	1.33879
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Measured			4771.21	5961.43	1.24946
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Ranked	Subtracted	0	11064.2	9897.84	1166.36
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Measured			154	0	154
208	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Ranked		1	240.782	265.717	24.935
	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	Squared		0	2572.14	2869.96	297.82
	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	Rooted	Divided	1	46.901	53.624	1.14334
	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	Squared	Subtracted		62783.5	50784.1	11999.4
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Ranked	Divided	0	11846.3	10638.4	1.11354
	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	Measured	Subtracted	1	10599.9	12064.7	1464.8
	cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]	Squared	Divided		70525.9	52678.7	1.33879
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Measured	Subtracted	0	5891.28	5737.71	153.57
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]		Divided		6596.23	5540.2	1.19061
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Rooted			23.8735	20.9532	1.13937
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Ranked	Subtracted		19939	18778	1161
	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]		Divided	1	285.684	252.234	1.13261
	septin 10 isoform 1. [refseq;acc:nm_144710]	Rooted	Subtracted		113.733	123.871	10.138
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Squared	Divided	0	75446.7	105900	1.40364
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Rooted	Subtracted		35.7516	38.4588	2.7072
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Measured	Divided	1	4068.78	5082.18	1.24907
209	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	Squared	Subtracted		62757.7	50767.8	11989.9
	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	Ranked			240.782	265.717	24.935
	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]	Rooted	Divided		46.8525	53.5324	1.14257
	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]	Squared			70525.9	52678.7	1.33879
	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]	Ranked			285.684	252.234	1.13261
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Rooted	Subtracted		121.695	131.815	10.12
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Squared		0	1487.24	1783.26	296.02
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Rooted	Divided		17.9668	15.7772	1.13878
	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	Measured	Subtracted		198.964	351.772	152.808
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	Rooted			46.9819	44.2892	2.6927
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Measured		1	11383.2	9926.61	1456.59
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]		Divided	0	93.5	111	1.18717
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Ranked			775	696	1.11351
	tigger transposable element derived 6. [refseq;acc:nm_030953]		Subtracted		12360	11200.2	1159.8
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Measured	Divided	1	4068.78	5082.18	1.24907
	zinc finger protein 277. [swissprot;acc:q9nrm2]	Squared		0	75446.7	105900	1.40364
210	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Rooted	Subtracted		26.0693	28.761	2.6917
	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Squared		1	36359.2	24466.8	11892.4
	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Rooted	Divided		46.8525	53.5316	1.14256
	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Ranked			285.684	252.234	1.13261
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Rooted	Subtracted		121.695	131.815	10.12
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Measured			4355.61	5810.82	1455.21
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Ranked	Divided	0	17144.8	15405.6	1.11289
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	Squared	Subtracted		677.989	382.311	295.678
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Measured			606.485	454.837	151.648
	rna-binding protein. [refseq;acc:nm_019027]	Ranked		1	237.302	212.41	24.892
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Squared	Divided		69549	92953.5	1.33652
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Ranked	Subtracted	0	12364.7	11207.7	1157
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Rooted	Divided		11.7534	10.3214	1.13874

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.