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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1108 to 1157 of 16578 in total 
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison	
277	RPL4	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	Subtracted	High confidence	239.277	262.434	23.157	
278	BEST2	vitelliform macular dystrophy 2-like protein 1. [source:refseq;acc:nm_017682]	Subtracted	Low confidence	37.9984	29.1831	8.8153	
278	MYEF2	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	Subtracted	High confidence	235.383	258.476	23.093	
278	RPS11	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Divided	High confidence	241.399	267.088	1.10642	
278	SLC7A10	asc-type amino acid transporter 1 (asc-1). [source:swissprot;acc:q9ns82]	Divided	Low confidence	205.006	196.369	1.04398	
279	BTBD14B	transcriptional repressor nac1. [source:refseq;acc:nm_052876]	Divided	Low confidence	202.309	211.2	1.04395	
279	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Subtracted	Low confidence	210.132	201.397	8.735	
279	PUS1	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	Subtracted	High confidence	242.66	265.715	23.055	
279	RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Divided	High confidence	252.644	228.42	1.10605	
280	LAPTM4B	lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [source:refseq;acc:nm_018407]	Subtracted	Low confidence	210	201.325	8.675	
280	MTA1	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Divided	High confidence	252.512	228.356	1.10578	
280	TFCP2L1	lbp-9. [source:refseq;acc:nm_014553]	Divided	Low confidence	219.758	210.509	1.04394	
280	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Subtracted	High confidence	267.208	244.168	23.04	
281		60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Divided	High confidence	241.808	267.335	1.10557	
281	MRPL12	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	Subtracted	High confidence	242.159	265.104	22.945	
281	TFCP2	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	Divided	Low confidence	219.749	210.503	1.04392	
281	TMEM115	pl6 protein (placental protein 6). [source:swissprot;acc:q12893]	Subtracted	Low confidence	209.995	201.322	8.673	
282	AMY1C	alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [source:swissprot;acc:p04745]	Divided	Low confidence	219.742	210.498	1.04391	
282	LAPTM4A	lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [source:swissprot;acc:q15012]	Subtracted	Low confidence	209.995	201.322	8.673	
282	NUDT12	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	Subtracted	High confidence	242.159	265.104	22.945	
282	RBBP4	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	Divided	High confidence	252.39	228.297	1.10553	
283	KHDRBS2	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Subtracted	Low confidence	209.31	200.66	8.65	
283	MRPL11	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	Subtracted	High confidence	242.37	265.255	22.885	
283	RPL11	60s ribosomal protein l11. [source:swissprot;acc:p39026]	Divided	High confidence	241.828	267.346	1.10552	
283	UBP1	upstream binding protein 1 (lbp-1a). [source:refseq;acc:nm_014517]	Divided	Low confidence	219.722	210.484	1.04389	
284	BCAR1	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Divided	High confidence	224.657	203.235	1.10541	
284	POLR3A	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	Subtracted	High confidence	242.686	265.516	22.83	
284	SLC7A10	asc-type amino acid transporter 1 (asc-1). [source:swissprot;acc:q9ns82]	Subtracted	Low confidence	205.006	196.369	8.637	
284	TNKS2	tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [source:swissprot;acc:q9h2k2]	Divided	Low confidence	214.675	205.692	1.04367	
285	CCT4	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Divided	High confidence	224.647	203.242	1.10532	
285	POLR1A	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	Subtracted	High confidence	242.691	265.481	22.79	
285	TAF4	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [source:swissprot;acc:o00268]	Divided	Low confidence	202.354	211.175	1.04359	
285	TPM4	tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [source:swissprot;acc:p07226]	Subtracted	Low confidence	201.219	192.595	8.624	
286	HOMER3	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Subtracted	Low confidence	210.057	201.45	8.607	
286	NEDD9	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Divided	High confidence	224.633	203.251	1.1052	
286	RPL30	60s ribosomal protein l30. [source:swissprot;acc:p04645]	Subtracted	High confidence	242.593	265.365	22.772	
286	TAF4B	transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [source:swissprot;acc:q92750]	Divided	Low confidence	202.356	211.174	1.04358	
287	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Divided	Low confidence	210.132	201.397	1.04337	
287	HOMER1	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Subtracted	Low confidence	210.05	201.454	8.596	
287	RPS4Y2	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Divided	High confidence	240.758	266.079	1.10517	
287	SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Subtracted	High confidence	225.217	202.459	22.758	
288		40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Divided	High confidence	240.758	266.078	1.10517	
288	DICER1	endoribonuclease dicer (ec 3.1.26.-) (helicase with rnase motif) (helicase-moi). [source:swissprot;acc:q9upy3]	Subtracted	Low confidence	208.915	200.322	8.593	
288	SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Divided	Low confidence	200.288	192.004	1.04314	
288	STX10	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	Subtracted	High confidence	234.691	257.442	22.751	
289		hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Divided	High confidence	272.781	246.892	1.10486	
289	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Subtracted	Low confidence	57.395	48.8186	8.5764	
289	KHDRBS2	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Divided	Low confidence	209.31	200.66	1.04311	
289	STX6	syntaxin 6. [source:swissprot;acc:o43752]	Subtracted	High confidence	234.673	257.414	22.741	
290		suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	Subtracted	High confidence	242.109	264.79	22.681	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/