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 1630 to 1679 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
204	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Rooted	1	55.8956	63.9636	1.14434
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Squared	1	12326.4	16522.9	1.34045
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Measured	0	7981.68	6685.11	1.19395
205	60s ribosomal protein l23a. [swissprot;acc:p29316]	Ranked	0	11844.9	10636.3	1.11363
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Ranked	1	228.1	200.968	1.13501
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Squared		12326.4	16522.9	1.34045
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Measured		4512.19	5655.52	1.25339
		Rooted		55.8956	63.9636	1.14434
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Measured	0	5418.2	4543.75	1.19245
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Rooted		23.8722	20.9337	1.14037
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Squared		99.0201	139.876	1.4126
206	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Measured	1	5720.25	4577.5	1.24965
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Squared	1	12326.4	16522.9	1.34045
	espin. [refseq;acc:nm_031475]	Rooted	0	23.8722	20.934	1.14036
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Rooted	1	140.508	122.878	1.14348
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Ranked	0	7479	6716	1.11361
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Ranked	1	228.085	201.006	1.13472
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Measured	0	1124.15	943.423	1.19157
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Squared	0	8.27667	5.86733	1.41064
207	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Rooted	1	140.508	122.878	1.14348
	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Squared	0	73080.8	102814	1.40685
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Measured		403.827	339.154	1.19069
	dc11 protein. [refseq;acc:nm_020186]	Ranked		7479	6716	1.11361
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Ranked	1	285.684	252.234	1.13261
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Rooted	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
208	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	Rooted		46.901	53.624	1.14334
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Ranked	0	11846.3	10638.4	1.11354
	cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]	Squared	1	70525.9	52678.7	1.33879
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Measured	0	6596.23	5540.2	1.19061
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Rooted	0	23.8735	20.9532	1.13937
	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]	Ranked	1	285.684	252.234	1.13261
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Squared	0	75446.7	105900	1.40364
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Measured	1	4068.78	5082.18	1.24907
209	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		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
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Rooted	0	17.9668	15.7772	1.13878
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Measured		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
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Measured	1	4068.78	5082.18	1.24907
	zinc finger protein 277. [swissprot;acc:q9nrm2]	Squared	0	75446.7	105900	1.40364
210	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Rooted	1	46.8525	53.5316	1.14256
	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Ranked	1	285.684	252.234	1.13261
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Ranked	0	17144.8	15405.6	1.11289
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Squared	1	69549	92953.5	1.33652
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Rooted	0	11.7534	10.3214	1.13874
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Squared		177.23	126.355	1.40264
	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	Measured		1053.33	887.413	1.18697

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/