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 2601 to 2650 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
326	60s ribosomal protein l5. [swissprot;acc:p46777]	Ranked	1	241.899	265.924	1.09932
	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366]	Squared	1	69124.3	54897.4	1.25915
	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Rooted	0	83.9673	88.8829	1.05854
	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	Measured	1	3432.96	4081.21	1.18883
	chromodomain y-like protein 2. [refseq;acc:nm_152342]	Measured	0	3053.31	2799.81	1.09054
	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	Ranked		11948.4	11295.6	1.05779
	germ cell-less. [refseq;acc:nm_022471]	Squared		3567.33	3084.18	1.15665
	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	Rooted	1	50.3803	45.4193	1.10923
327	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	Ranked	0	9897.29	10466.5	1.05751
	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	Squared	0	178.482	205.335	1.15045
	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]	Rooted	1	50.3803	45.4193	1.10923
	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	Measured	0	175.644	161.091	1.09034
	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Ranked	1	243.817	267.962	1.09903
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Squared	1	16424.1	20645.8	1.25704
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	Rooted	0	23.6959	25.0734	1.05813
	septin 10 isoform 1. [refseq;acc:nm_144710]	Measured	1	16067.4	19094.4	1.18839
328	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	Squared	0	6747.71	5878.56	1.14785
	60s ribosomal protein l12. [swissprot;acc:p30050]	Measured	0	1657.78	1805.05	1.08884
	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	Ranked	1	258.437	235.183	1.09888
	brain protein 44. [swissprot;acc:o95563]	Measured	1	15999.1	19007.1	1.18801
	histone h4. [swissprot;acc:p02304]	Rooted	0	98.5525	104.126	1.05655
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Squared	1	16442.8	20662.7	1.25664
	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	Rooted	1	50.3803	45.4193	1.10923
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Ranked	0	10897	11520	1.05717
329	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Squared	0	195397	170319	1.14724
	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]	Rooted	1	50.3803	45.4193	1.10923
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Measured	0	1658.07	1805.36	1.08883
	metaxin 2. [swissprot;acc:o75431]	Squared	1	41236	51807	1.25635
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Ranked		312	284	1.09859
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	Measured		15999.1	19007.1	1.18801
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	Ranked	0	15977.3	15115.5	1.05701
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Rooted		15.4404	16.3116	1.05642
330	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Measured		1658.23	1805.52	1.08882
	60s ribosomal protein l32. [swissprot;acc:p02433]	Rooted	1	50.519	45.5497	1.1091
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Ranked	1	312	284	1.09859
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Rooted	0	57.5016	60.7262	1.05608
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Squared	0	2758.07	3161.7	1.14635
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Squared	1	16203.4	20339.9	1.25529
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Ranked	0	12320.2	13018.5	1.05668
	septin 6. [swissprot;acc:q14141]	Measured	1	15959.9	18957.1	1.1878
331	40s ribosomal protein s3a. [swissprot;acc:p49241]	Ranked	0	10405.1	10992.4	1.05644
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Squared		26.2121	22.8932	1.14497
	alpha-nac protein. [sptrembl;acc:q9h009]	Rooted		9.95878	9.44328	1.05459
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Rooted	1	60.6697	67.2802	1.10896
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Ranked	1	312	284	1.09859
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Measured	0	4088	4451	1.0888
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Measured	1	20287.2	17083.8	1.18751
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Squared	1	33100.3	41520.6	1.25439
332	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Measured	0	15411.3	14167	1.08783
332	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Rooted	0	15.297	14.5086	1.05434

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.

- http://analysis.yellowcouch.org/