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.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 7308 to 7357 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
1827	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	Squared	21994.2	24133.1	1.09725
1828	fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787]	Ranked	202.41	200.115	1.01147
	heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626]	Measured	5633.44	5997	1.06454
	nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]	Squared	21994.2	24133.1	1.09725
	similar to trna synthetase class ii. [refseq;acc:nm_152268]	Rooted	60.6845	62.5302	1.03041
1829	cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708]	Ranked	212.884	215.323	1.01146
	ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830]	Measured	5633.44	5997	1.06454
	ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153]	Squared	21994.2	24133.1	1.09725
	vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7]	Rooted	61.1874	63.0474	1.0304
1830	6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237]	Ranked	240.32	243.069	1.01144
	60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809]	Rooted	60.2038	62.0316	1.03036
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Measured	5633.44	5997	1.06454
	dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992]	Squared	21994.2	24133.1	1.09725
1831	26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	Rooted	63.0811	64.9964	1.03036
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Ranked	214.746	212.328	1.01139
	solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3]	Measured	5633.44	5997	1.06454
	survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893]	Squared	21994.2	24133.1	1.09725
1832	adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326]	Rooted	63.1745	65.0927	1.03036
	dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733]	Measured	5633.44	5997	1.06454
	probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6]	Squared	21994.2	24133.1	1.09725
	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	Ranked	180.409	182.459	1.01136
1833	5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914]	Measured	6175.23	6572.85	1.06439
	cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]	Ranked	180.409	182.459	1.01136
	ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636]	Rooted	65.5142	67.5007	1.03032
	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	Squared	21999.1	24137.4	1.0972
1834	60s ribosomal protein l11. [swissprot;acc:p39026]	Measured	3593.24	3375.93	1.06437
	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]	Ranked	180.409	182.459	1.01136
	ral-a exchange factor ralgps2. [refseq;acc:nm_152663]	Rooted	65.5142	67.5007	1.03032
	transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014]	Squared	22002	24139.9	1.09717
1835	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	Ranked	194.573	192.396	1.01132
	p47 protein isoform a. [refseq;acc:nm_016143]	Squared	31818	34894.4	1.09669
	stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861]	Rooted	65.5142	67.5007	1.03032
	transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560]	Measured	5019.3	5342.36	1.06436
1836	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566]	Rooted	72.5251	74.7236	1.03031
	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	Squared	26653	29227.4	1.09659
	ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247]	Ranked	208.821	211.17	1.01125
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Measured	5019.3	5342.36	1.06436
1837	cerebral cell adhesion molecule. [refseq;acc:nm_016174]	Rooted	77.9868	80.3483	1.03028
	ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053]	Ranked	218.984	221.446	1.01124
	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	Measured	5739.49	6108.72	1.06433
	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]	Squared	26653	29227.4	1.09659
1838	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]		12666.8	13887.8	1.09639
	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Measured	5739.49	6108.72	1.06433
	proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436]	Rooted	61.5765	63.4381	1.03023
	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	Ranked	218.984	221.446	1.01124
1839	atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010]	Measured	5739.49	6108.72	1.06433
	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	Squared	12666.8	13887.8	1.09639
	eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042]	Ranked	221.525	224.001	1.01118
	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	Rooted	72.2983	74.4769	1.03013
1840	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	Measured	3591.95	3375.34	1.06417

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.