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 1600 to 1649 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
200	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	Squared	0	5317.39	3738.08	1.42249
201	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		0	351.996	499.177	1.41813
	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]		1	71033.4	95440.2	1.3436
	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]	Rooted	1	61.2893	70.3856	1.14842
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Rooted	0	23.8722	20.9336	1.14038
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Ranked	0	16853	15123	1.1144
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Ranked	1	240.133	211.382	1.13601
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	Measured	0	6804.88	5690.63	1.1958
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Measured	1	4810.22	6075.04	1.26294
202	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	Squared	1	71030.1	95434.8	1.34358
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Measured	0	606.049	723.75	1.19421
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Squared	0	3339.18	2360.97	1.41433
	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	Measured	1	4812.01	6076.09	1.26269
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Rooted	0	23.8722	20.9336	1.14038
	serpin b11. [swissprot;acc:q96p15]	Ranked	0	16853	15123	1.1144
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Ranked	1	201.478	228.784	1.13553
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Rooted		57.3527	65.7973	1.14724
203	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	Measured		11757.8	9352.11	1.25723
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	Ranked	0	16853	15123	1.1144
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Ranked	1	201.515	228.752	1.13516
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Squared	0	93.5732	66.2405	1.41263
	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	Squared	1	20988.2	15632.1	1.34263
	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]	Measured	0	304	363	1.19408
	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Rooted	0	22.1344	25.2414	1.14037
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Rooted	1	46.3291	53.1063	1.14628
204	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Ranked	0	15081.8	16802.1	1.11406
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Squared		94.1723	66.6659	1.4126
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Rooted		23.8722	20.9337	1.14037
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	Ranked	1	201.515	228.752	1.13516
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Measured		4512.19	5655.52	1.25339
		Rooted		55.8956	63.9636	1.14434
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Squared		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

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/