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 8214 to 8263 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
2054	glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2]	Rooted	65.5449	67.2768	1.02642
	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	Ranked	207.665	205.948	1.00834
	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]	Measured	5634.8	5952.7	1.05642
2055	copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656]	Squared	26619	29013.9	1.08997
	dymeclin. [refseq;acc:nm_017653]	Ranked	218.79	216.981	1.00834
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Rooted	62.3777	64.0227	1.02637
	possible global transcription activator snf2l1. [swissprot;acc:p28370]	Measured	5634.8	5952.7	1.05642
2056	copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670]	Squared	26621.3	29016.2	1.08996
	sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]	Ranked	218.79	216.981	1.00834
	tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981]	Measured	5634.8	5952.7	1.05642
	zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312]	Rooted	62.3777	64.0227	1.02637
2057	elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
	lats homolog 1. [refseq;acc:nm_004690]	Ranked	218.79	216.981	1.00834
	possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]	Measured	5634.8	5952.7	1.05642
	tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7]	Squared	24214.1	26392.2	1.08995
2058	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	Measured	5552.69	5865.84	1.0564
	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457]	Rooted	74.9362	76.9113	1.02636
	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	Squared	25226.2	27492	1.08982
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	Ranked	218.79	216.981	1.00834
2059	26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210]	Rooted	74.9362	76.9113	1.02636
	adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747]	Measured	5552.69	5865.84	1.0564
	interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894]	Squared	24224.6	26398.4	1.08974
	nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]	Ranked	218.79	216.981	1.00834
2060	adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3]	Measured	5552.69	5865.84	1.0564
	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	Squared	24224.5	26398.4	1.08974
	dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]	Ranked	218.79	216.981	1.00834
	nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991]	Rooted	66.825	68.5831	1.02631
2061	adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382]	Measured	5552.69	5865.84	1.0564
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Squared	24225.6	26399	1.08972
	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]	Rooted	66.825	68.5831	1.02631
	tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]	Ranked	218.79	216.981	1.00834
2062	adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843]	Measured	5552.7	5865.85	1.0564
	germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]	Rooted	66.825	68.5831	1.02631
	tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]	Ranked	218.79	216.981	1.00834
	zinc finger protein 258. [refseq;acc:nm_145310]	Squared	24225.6	26399	1.08972
2063	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4]	Rooted	65.2079	66.9218	1.02628
	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	Ranked	207.638	205.923	1.00833
	swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074]	Measured	5634.63	5952.14	1.05635
	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]	Squared	24225.6	26399	1.08972
2064	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	Rooted	62.2279	63.8594	1.02622
	adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567]	Measured	5548.79	5861.31	1.05632
	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	Ranked	207.655	205.939	1.00833
	zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]	Squared	24225.6	26399	1.08972
2065	60s ribosomal protein l35. [swissprot;acc:p42766]	Measured	3602.25	3410.23	1.05631
	actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]	Squared	24225.6	26399	1.08972
	swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074]	Rooted	61.0898	62.6908	1.02621
	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	Ranked	214.328	212.561	1.00831
2066	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]	Squared	24225.6	26399	1.08972
	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	Ranked	229.102	231.001	1.00829
	ring finger protein 20. [refseq;acc:nm_019592]	Rooted	59.5914	61.1533	1.02621

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.