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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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Rank	description	Gene	Hugo	Network Comparison Type	Value Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 532 to 581 of 6456 in total

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

Rank	description	Hugo	Network Comparison Type	red	green	network_comparison
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	SIN3A	Divided	241.07	267.88	1.11121
267	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	no value	Subtracted	243.12	266.661	23.541
	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]	DENR	Divided	241.07	267.88	1.11121
268	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	EIF5		271.016	244.167	1.10996
	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	PRMT3	Subtracted	241.625	265.136	23.511
269	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	no value
	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	PCYT1A	Divided	241.373	267.352	1.10763
270	40s ribosomal protein s3. [swissprot;acc:p23396]	RPS3	Subtracted	241.612	265.119	23.507
	fad synthetase. [refseq;acc:nm_025207]	FLAD1	Divided	241.373	267.352	1.10763
271	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	no value
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	SEC61G	Subtracted	243.072	266.559	23.487
272	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	LGTN	Divided	241.373	267.352	1.10763
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	MRPL17	Subtracted	242.83	266.248	23.418
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]	PAPSS1	Divided	241.373	267.352	1.10763
	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	POLR2B	Subtracted	243.208	266.617	23.409
274	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	MRPL36		242.744	266.07	23.326
	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	POR	Divided	241.373	267.352	1.10763
275	40s ribosomal protein s5. [swissprot;acc:p46782]	RPS5	Subtracted	242.473	265.756	23.283
	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]	PCYT1B	Divided	241.373	267.352	1.10763
276	60s ribosomal protein l32. [swissprot;acc:p02433]	SNORA7A		241.13	266.969	1.10716
	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	DDX24	Subtracted	258.437	235.183	23.254
277	40s ribosomal protein s29. [swissprot;acc:p30054]	no value	Divided	241.849	267.642	1.10665
	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	RPL4	Subtracted	239.277	262.434	23.157
278	40s ribosomal protein s11. [swissprot;acc:p04643]	RPS11	Divided	241.399	267.088	1.10642
	myelin gene expression factor 2. [refseq;acc:nm_016132]	MYEF2	Subtracted	235.383	258.476	23.093
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	RBBP7	Divided	252.644	228.42	1.10605
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	PUS1	Subtracted	242.66	265.715	23.055
280	metastasis-associated protein mta1. [swissprot;acc:q13330]	MTA1	Divided	252.512	228.356	1.10578
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	TFDP2	Subtracted	267.208	244.168	23.04
281	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	MRPL12		242.159	265.104	22.945
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	no value	Divided	241.808	267.335	1.10557
282	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). [swissprot;acc:q09028]	RBBP4		252.39	228.297	1.10553
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	NUDT12	Subtracted	242.159	265.104	22.945
283	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	MRPL11		242.37	265.255	22.885
	60s ribosomal protein l11. [swissprot;acc:p39026]	RPL11	Divided	241.828	267.346	1.10552
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	BCAR1		224.657	203.235	1.10541
	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	POLR3A	Subtracted	242.686	265.516	22.83
285	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	POLR1A		242.691	265.481	22.79
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	CCT4	Divided	224.647	203.242	1.10532
286	60s ribosomal protein l30. [swissprot;acc:p04645]	RPL30	Subtracted	242.593	265.365	22.772
	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]	NEDD9	Divided	224.633	203.251	1.1052
287	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	RPS4Y2		240.758	266.079	1.10517
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	SF3B1	Subtracted	225.217	202.459	22.758
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	no value	Divided	240.758	266.078	1.10517
	syntaxin 10 (syn10). [swissprot;acc:o60499]	STX10	Subtracted	234.691	257.442	22.751
289	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	no value	Divided	272.781	246.892	1.10486
	syntaxin 6. [swissprot;acc:o43752]	STX6	Subtracted	234.673	257.414	22.741
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	RRM2	Divided	231.969	210.064	1.10428
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	no value	Subtracted	242.109	264.79	22.681
291	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	AK2		241.509	264.163	22.654

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
- 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.