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

Results: HTML CSV LaTeX

Showing element 580 to 629 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Hugo	red	green	network_comparison
580	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	ZNRD1	236.751	252.038	1.06457
581	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	TLX3	237.28	252.492	1.06411
582	homeobox protein barh-like 1. [swissprot;acc:q9hbu1]	BARX1
583	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]	OPN4
584	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]	TLX2
585	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]	TLX1
586	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]	HECTD1
587	homeobox protein barh-like 2. [swissprot;acc:q9umq3]	BARX2
588	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	SBDS	216.557	230.362	1.06375
589	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	no value	228.215	214.546	1.06371
590	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	RRM1	217.215	204.279	1.06333
591	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	RPP30	216.72	230.439	1.0633
592	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	PPP1R7	91.63	97.4011	1.06298
593	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	DR1	232.118	218.406	1.06278
594	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	CDC40	223.282	210.136	1.06256
595	vav proto-oncogene. [swissprot;acc:p15498]	VAV1	212.2	199.849	1.0618
596	vav-3 protein. [swissprot;acc:q9ukw4]	VAV3	212.253	199.908	1.06175
597	vav-2 protein. [swissprot;acc:p52735]	VAV2	212.526	200.212	1.0615
598	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	AKT1	248.463	234.095	1.06138
599	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]	AKT3
600	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	AKT2
601	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	VPS39	206.274	218.792	1.06069
602	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]	MAP4
603	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	LEF1	225.829	212.945	1.0605
604	60s ribosomal protein l15. [swissprot;acc:p39030]	RPL15	217.862	230.978	1.0602
605	histone h2b.c (h2b/c). [swissprot;acc:q99880]	HIST1H2BL	247.47	233.441	1.0601
606	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	HIST2H2BA
607	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	no value
608	histone h2b. [refseq;acc:nm_175055]
609	histone h2b.s (h2b/s). [swissprot;acc:p57053]
610	histone h2b.d (h2b/d). [swissprot;acc:q99877]
611	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	HIST3H3
612	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]	HIST1H2BA
613	histone h2b.e (h2b/e). [swissprot;acc:q99879]	no value
614	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	HOXA10	214.257	202.125	1.06002
615	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]	HOXB9		202.132	1.05999
616	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	HOXA9
617	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	HOXC9		202.135	1.05997
618	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	GABRG3	214.256	202.139	1.05994
619	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	FOXG1
620	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	GABRG1		202.14
621	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]	GABRA2
622	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]	GABRA6
623	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]	GABRG2
624	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	no value		202.139
625	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]	GABRA4		202.14
626	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]	GABRE
627	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	JMJD6		202.139
628	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]	GABRA1		202.14
629	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]	GABRA3

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.