Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1377 to 1426 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
689	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	Divided	6920.69	7747.63	1.11949	
689	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	Subtracted	6311.6	6989.33	677.73	
690	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	Divided	6920.69	7747.63	1.11949	
690	trna isopentenylpyrophosphate transferase. [source:refseq;acc:nm_017646]	Subtracted	6257.99	6932.95	674.96	
691	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	Divided	6920.69	7747.63	1.11949	
691	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [source:swissprot;acc:p48643]	Subtracted	8425.35	7751.57	673.78	
692	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	Divided	6920.69	7747.63	1.11949	
692	e-1 enzyme. [source:refseq;acc:nm_021204]	Subtracted	6603.09	7274.72	671.63	
693	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Subtracted	3199.4	3870.8	671.4	
693	j kappa-recombination signal binding protein (rbp-j kappa). [source:swissprot;acc:q06330]	Divided	7725.1	8647.74	1.11943	
694	human immunodeficiency virus type i enhancer binding protein 3. [source:refseq;acc:nm_024503]	Divided	7725.1	8647.74	1.11943	
694	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	Subtracted	6075.55	6746.92	671.37	
695	vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [source:swissprot;acc:p27449]	Subtracted	5768.32	6434.78	666.46	
695	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [source:swissprot;acc:p15822]	Divided	7725.1	8647.74	1.11943	
696	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [source:swissprot;acc:p31629]	Divided	7725.1	8647.74	1.11943	
696	sarcoglycan zeta; zeta-sarcoglycan. [source:refseq;acc:nm_139167]	Subtracted	5768.32	6434.78	666.46	
697	golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [source:refseq;acc:nm_022735]	Subtracted	5768.32	6434.78	666.46	
697	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [source:swissprot;acc:q99962]	Divided	7105.27	7953.71	1.11941	
698	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	Divided	7101.95	7949.85	1.11939	
698	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q92629]	Subtracted	5768.32	6434.78	666.46	
699	cellular modulator of immune recognition. [source:refseq;acc:nm_145021]	Subtracted	5768.32	6434.78	666.46	
699	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	Divided	7101.94	7949.84	1.11939	
700	40s ribosomal protein s28. [source:swissprot;acc:p25112]	Divided	7161.14	8015.92	1.11936	
700	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [source:swissprot;acc:q99437]	Subtracted	5768.32	6434.78	666.46	
701	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q13326]	Subtracted	5768.32	6434.78	666.46	
701	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [source:swissprot;acc:p55060]	Divided	7802.31	8731.82	1.11913	
702	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	Divided	7067.46	7909.27	1.11911	
702	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	Subtracted	5549.2	6215.42	666.22	
703	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	Divided	6912.56	7735.12	1.11899	
703	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	Subtracted	5549.2	6215.42	666.22	
704	alpha-nac protein. [source:sptrembl;acc:q9h009]	Divided	6912.27	7734.68	1.11898	
704	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	Subtracted	5549.2	6215.42	666.22	
705	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	Divided	6912.09	7734.41	1.11897	
705	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	Subtracted	5549.2	6215.42	666.22	
706	di-ras2. [source:refseq;acc:nm_017594]	Divided	6912.08	7734.39	1.11897	
706	syntaxin 12. [source:refseq;acc:nm_177424]	Subtracted	5552.92	6217.59	664.67	
707	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	Subtracted	5870.2	6533.39	663.19	
707	c18b11 homolog (44.9kd). [source:refseq;acc:nm_152260]	Divided	5317.78	5944.25	1.11781	
708	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	Subtracted	4775.11	5438.18	663.07	
708	z-protein (protein cgi-119) (s1r protein). [source:swissprot;acc:q9hc24]	Divided	5317.78	5944.25	1.11781	
709	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	Subtracted	5148.71	5811.74	663.03	
709	pp1201 protein. [source:refseq;acc:nm_022152]	Divided	5317.78	5944.25	1.11781	
710	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Subtracted	2755.15	2094.3	660.85	
710	lifeguard; kiaa0950 protein. [source:refseq;acc:nm_012306]	Divided	5317.78	5944.25	1.11781	
711	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Subtracted	2759.61	2099.49	660.12	
711	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	Divided	5317.78	5944.25	1.11781	
712	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	Subtracted	2760.28	2100.27	660.01	
712	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [source:swissprot;acc:p36956]	Divided	5317.78	5944.25	1.11781	
713	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	Subtracted	5162.52	5822.47	659.95	
713	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	Divided	3996.81	4465.61	1.11729	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/