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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1375 to 1424 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
172	williams beuren syndrome chromosome region 20c isoform 1. [source:refseq;acc:nm_032158]	Measured	0	112.666	141.702	1.25772	
172	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	Ranked	0	12225.7	13893.1	1.13638	
173	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Rooted	1	145.551	168.796	1.1597	
173	60s ribosomal protein l7. [source:swissprot;acc:p18124]	Rooted	0	27.512	31.7228	1.15305	
173	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Measured	1	4579.34	5940.64	1.29727	
173	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Measured	0	3265.25	4102.97	1.25656	
173	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2]	Squared	0	48.239	75.2348	1.55963	
173	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Squared	1	82624.3	115061	1.39258	
173	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Ranked	1	227.032	193.056	1.17599	
173	suppressor of actin 1. [source:refseq;acc:nm_014016]	Ranked	0	19088.1	16804.6	1.13589	
174	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [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)]. [source:swissprot;acc:o95340]	Rooted	0	15.8745	18.303	1.15298	
174	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	Squared	0	48.3438	75.3968	1.5596	
174	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Ranked	1	335	286	1.17133	
174	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	Measured	0	488.43	612.604	1.25423	
174	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Measured	1	4455.95	5774.03	1.2958	
174	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Rooted	1	145.551	168.796	1.1597	
174	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [source:refseq;acc:nm_006916]	Ranked	0	13248.5	11666.4	1.13561	
174	sedlin. [source:swissprot;acc:o14582]	Squared	1	112820	157033	1.39189	
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Ranked	1	199.949	234.187	1.17123	
175	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [source:refseq;acc:nm_015247]	Measured	0	1382.5	1107	1.24887	
175	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Squared	0	48.5538	75.7214	1.55954	
175	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Measured	1	4456.67	5773.77	1.29553	
175	nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	Rooted	0	61.6393	70.9983	1.15183	
175	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Rooted	1	145.551	168.796	1.1597	
175	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Squared	1	112820	157033	1.39189	
175	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [source:refseq;acc:nm_022445]	Ranked	0	13248.5	11666.4	1.13561	
176	bet3 homolog. [source:swissprot;acc:o43617]	Squared	1	112820	157033	1.39189	
176	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	Squared	0	48.5538	75.7214	1.55954	
176	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Ranked	0	13068	11528	1.13359	
176	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_032959]	Rooted	0	20.3469	17.7078	1.14904	
176	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Ranked	1	275.754	235.908	1.1689	
176	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Measured	1	4456.93	5773.67	1.29544	
176	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Rooted	1	145.551	168.796	1.1597	
176	small glutamine rich protein with tetratricopeptide repeats 2. [source:refseq;acc:nm_019072]	Measured	0	3023.85	2436.4	1.24111	
177	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	Measured	0	4131.06	3340.03	1.23683	
177	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Ranked	1	229.406	196.695	1.1663	
177	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_145325]	Rooted	0	20.3458	17.7104	1.14881	
177	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [source:refseq;acc:nm_023934]	Squared	0	73.1683	109.766	1.50019	
177	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Measured	1	4457.06	5773.63	1.29539	
177	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Rooted	1	145.551	168.796	1.1597	
177	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Ranked	0	14922.7	13174.5	1.1327	
177	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Squared	1	78383	108483	1.38401	
178	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Squared	1	25326.4	18354.1	1.37988	
178	collagen alpha 5(iv) chain precursor. [source:swissprot;acc:p29400]	Rooted	0	35.0775	30.5361	1.14872	
178	dc11 protein. [source:refseq;acc:nm_020186]	Squared	0	73.1683	109.766	1.50019	
178	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	Measured	0	498.07	615.233	1.23523	
178	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Ranked	1	226.887	194.72	1.1652	
178	integral membrane protein cii-3b. [source:sptrembl;acc:o75609]	Ranked	0	14951.6	13204.2	1.13234	
178	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Measured	1	21591.5	27904.5	1.29238	
178	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Rooted	1	45.7414	52.932	1.1572	

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/