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

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 530 to 579 of 6456 in total

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

Rank	Hugo	Network Comparison Type	description	red	network_comparison	green
265	SF3B1	Divided	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	225.217	1.11241	202.459
266	RPL10L	Subtracted	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	243.12	23.542	266.662
	SIN3A	Divided	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	241.07	1.11121	267.88
267	no value	Subtracted	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12	23.541	266.661
	DENR	Divided	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]	241.07	1.11121	267.88
268	EIF5		eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	271.016	1.10996	244.167
	PRMT3	Subtracted	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	241.625	23.511	265.136
269	no value		40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
	PCYT1A	Divided	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	241.373	1.10763	267.352
270	FLAD1		fad synthetase. [refseq;acc:nm_025207]
	RPS3	Subtracted	40s ribosomal protein s3. [swissprot;acc:p23396]	241.612	23.507	265.119
271	no value	Divided	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]	241.373	1.10763	267.352
	SEC61G	Subtracted	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	243.072	23.487	266.559
272	LGTN	Divided	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	241.373	1.10763	267.352
	MRPL17	Subtracted	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	242.83	23.418	266.248
273	PAPSS1	Divided	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]	241.373	1.10763	267.352
	POLR2B	Subtracted	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	243.208	23.409	266.617
274	MRPL36		60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	242.744	23.326	266.07
	POR	Divided	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	241.373	1.10763	267.352
275	PCYT1B		cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
	RPS5	Subtracted	40s ribosomal protein s5. [swissprot;acc:p46782]	242.473	23.283	265.756
276	DDX24		atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	258.437	23.254	235.183
	SNORA7A	Divided	60s ribosomal protein l32. [swissprot;acc:p02433]	241.13	1.10716	266.969
277	no value		40s ribosomal protein s29. [swissprot;acc:p30054]	241.849	1.10665	267.642
	RPL4	Subtracted	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	239.277	23.157	262.434
278	MYEF2		myelin gene expression factor 2. [refseq;acc:nm_016132]	235.383	23.093	258.476
	RPS11	Divided	40s ribosomal protein s11. [swissprot;acc:p04643]	241.399	1.10642	267.088
279	PUS1	Subtracted	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	242.66	23.055	265.715
	RBBP7	Divided	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	252.644	1.10605	228.42
280	MTA1		metastasis-associated protein mta1. [swissprot;acc:q13330]	252.512	1.10578	228.356
	TFDP2	Subtracted	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	267.208	23.04	244.168
281	no value	Divided	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	241.808	1.10557	267.335
	MRPL12	Subtracted	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	242.159	22.945	265.104
282	NUDT12		nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
	RBBP4	Divided	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]	252.39	1.10553	228.297
283	MRPL11	Subtracted	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	242.37	22.885	265.255
	RPL11	Divided	60s ribosomal protein l11. [swissprot;acc:p39026]	241.828	1.10552	267.346
284	BCAR1		crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	224.657	1.10541	203.235
	POLR3A	Subtracted	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	242.686	22.83	265.516
285	CCT4	Divided	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	224.647	1.10532	203.242
	POLR1A	Subtracted	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	242.691	22.79	265.481
286	NEDD9	Divided	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]	224.633	1.1052	203.251
	RPL30	Subtracted	60s ribosomal protein l30. [swissprot;acc:p04645]	242.593	22.772	265.365
287	RPS4Y2	Divided	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	240.758	1.10517	266.079
	SF3B1	Subtracted	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	225.217	22.758	202.459
288	no value	Divided	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	240.758	1.10517	266.078
	STX10	Subtracted	syntaxin 10 (syn10). [swissprot;acc:o60499]	234.691	22.751	257.442
289	no value	Divided	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	272.781	1.10486	246.892
	STX6	Subtracted	syntaxin 6. [swissprot;acc:o43752]	234.673	22.741	257.414
290	no value		suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	242.109	22.681	264.79

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.