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 [...,...].
Value Type Interaction Map description Network Comparison Type Rank Gene red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [source:swissprot;acc:q13813]	3038	0.00001	0.00001	1	
spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [source:swissprot;acc:q01082]	1602	5232.14	5605.8	1.07142	
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [source:swissprot;acc:o15020]	1601	5232.14	5605.8	1.07142	
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	968	7813.48	8570.11	1.09684	
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [source:refseq;acc:nm_005470]	1334	5804.75	6270.15	1.08018	
sperm tail protein shippo1; h-shippo 1. [source:refseq;acc:nm_053280]	2797	0.00001	0.00001	1	
spermatogenesis associated 6. [source:refseq;acc:nm_019073]	69	6475.5	10307.5	1.59177	
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [source:swissprot;acc:p19623]	1306	5500.92	5949.26	1.0815	
spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [source:swissprot;acc:p52788]	3118	0.00001	0.00001	1	
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [source:refseq;acc:nm_003676]	1238	5873.56	6370.31	1.08457	
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	7	1153.5	339.5	3.39764	
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]	472	9649.61	11053.5	1.14549	
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0]	485	9649.61	11053.5	1.14549	
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [source:refseq;acc:nm_003901]	1468	5473.09	5887.45	1.07571	
spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]	2879	0.00001	0.00001	1	
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	236	4723.53	5828.46	1.23392	
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [source:refseq;acc:nm_016333]	1958	5448.35	5777.35	1.06039	
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	649	5248.07	5901.72	1.12455	
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	296	4911.81	5909.18	1.20306	
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	648	5248.07	5901.72	1.12455	
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	191	4638.1	5923.4	1.27712	
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	348	4991.02	5885.09	1.17914	
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	207	4771.21	5961.43	1.24946	
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [source:swissprot;acc:q15427]	1224	4331.35	4700.91	1.08532	
splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	395	4532.73	5269.33	1.16251	
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	1976	5939.85	6294.91	1.05978	
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [source:swissprot;acc:q01081]	1959	5448.35	5777.35	1.06039	
splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [source:swissprot;acc:p26368]	1961	5448.35	5777.35	1.06039	
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	2549	4725.79	4824.4	1.02087	
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [source:swissprot;acc:p23152]	889	5903.18	6506.32	1.10217	
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [source:swissprot;acc:q12872]	2267	9146.11	8743.98	1.04599	
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [source:swissprot;acc:p23246]	2070	10178.5	9638.08	1.05607	
sporulation-induced transcript 4-associated protein. [source:refseq;acc:nm_018312]	1512	7234.61	7771.58	1.07422	
sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	676	5549.2	6215.42	1.12006	
sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	677	5549.2	6215.42	1.12006	
sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	675	5549.2	6215.42	1.12006	
sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	674	5549.2	6215.42	1.12006	
spry domain-containing socs box protein ssb-1. [source:refseq;acc:nm_025106]	2814	0.00001	0.00001	1	
spry domain-containing socs box protein ssb-4. [source:refseq;acc:nm_080862]	2806	0.00001	0.00001	1	
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [source:swissprot;acc:q14534]	2166	6952.66	7315.06	1.05212	
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [source:swissprot;acc:p29508]	1694	5767.69	6165.87	1.06904	
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	310	4909.79	5878.79	1.19736	
sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	2222	5309.65	5066.82	1.04793	
sr rich protein. [source:refseq;acc:nm_032870]	2257	6245.32	6534.23	1.04626	
ss18-like protein 1 (syt homolog-1). [source:swissprot;acc:o75177]	2766	0.00001	0.00001	1	
ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [source:swissprot;acc:q15532]	2942	0.00001	0.00001	1	
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [source:swissprot;acc:q9y3m8]	478	9649.61	11053.5	1.14549	
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [source:swissprot;acc:q96dr4]	1870	6076.66	6463.13	1.0636	
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [source:swissprot;acc:q9nsy2]	1865	6076.66	6463.12	1.0636	
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	1862	6076.66	6463.13	1.0636	

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/