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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 2458 to 2507 of 25824 in total 
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
308	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Ranked	Divided	242.153	266.673	1.10126	
308	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	Measured	Subtracted	11852.9	10773.5	1079.4	
308	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Rooted	Divided	50.4687	45.2733	1.11476	
308	necdin. [source:swissprot;acc:q99608]	Ranked	Subtracted	88.2482	110.265	22.0168	
308	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	Squared	Subtracted	32991.5	40704.5	7713	
308	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Rooted	Subtracted	65.9938	73.9449	7.9511	
308	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Measured	Divided	4977.09	5966.44	1.19878	
309	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [source:refseq;acc:nm_152414]	Measured	Subtracted	11848.8	10770.3	1078.5	
309	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Squared	Divided	28900.8	36762.6	1.27203	
309	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Ranked	Subtracted	88.2482	110.265	22.0168	
309	ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	Squared	Subtracted	32987.4	40698.5	7711.1	
309	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Ranked	Divided	242.153	266.673	1.10126	
309	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Rooted	Subtracted	65.9938	73.9449	7.9511	
309	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Measured	Divided	4977.8	5966.14	1.19855	
309	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Rooted	Divided	56.185	62.6036	1.11424	
310	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [source:swissprot;acc:q99943]	Measured	Subtracted	7551.8	8630.06	1078.26	
310	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Squared	Divided	28901.4	36762.1	1.27198	
310	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Ranked	Subtracted	88.2482	110.265	22.0168	
310	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Rooted	Divided	95.0526	85.3206	1.11406	
310	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Ranked	Divided	242.153	266.673	1.10126	
310	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	Squared	Subtracted	30651.3	38253.3	7602	
310	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Rooted	Subtracted	56.9506	64.7888	7.8382	
310	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]	Measured	Divided	4909.79	5878.79	1.19736	
311	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	Squared	Divided	30566.4	38866.5	1.27154	
311	40s ribosomal protein s28. [source:swissprot;acc:p25112]	Squared	Subtracted	30682.9	38183.6	7500.7	
311	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	Measured	Subtracted	2820.51	3897.1	1076.59	
311	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Ranked	Subtracted	88.2482	110.265	22.0168	
311	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Rooted	Divided	95.0526	85.3206	1.11406	
311	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Ranked	Divided	242.627	267.151	1.10108	
311	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Rooted	Subtracted	62.3337	70.0738	7.7401	
311	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Measured	Divided	4981.52	5964.58	1.19734	
312	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	Ranked	Divided	242.195	266.663	1.10103	
312	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [source:swissprot;acc:o14645]	Squared	Subtracted	33044.3	40524.8	7480.5	
312	max protein. [source:swissprot;acc:p25912]	Measured	Subtracted	4640.26	5704.87	1064.61	
312	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Ranked	Subtracted	88.2482	110.265	22.0168	
312	methyltransferase like 2. [source:refseq;acc:nm_018396]	Squared	Divided	71576.8	56326.7	1.27074	
312	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Rooted	Divided	95.0526	85.3206	1.11406	
312	nostrin. [source:refseq;acc:nm_052946]	Rooted	Subtracted	59.6399	51.9242	7.7157	
312	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Measured	Divided	4598.21	5500.48	1.19622	
313	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Squared	Divided	71576.8	56326.7	1.27074	
313	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Rooted	Subtracted	59.6399	51.9242	7.7157	
313	fibulin-2 precursor. [source:swissprot;acc:p98095]	Squared	Subtracted	45189.6	52666.2	7476.6	
313	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Ranked	Subtracted	88.2482	110.265	22.0168	
313	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Rooted	Divided	95.0526	85.3206	1.11406	
313	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Measured	Divided	21644.2	18098.7	1.1959	
313	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Ranked	Divided	232.473	211.207	1.10069	
313	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Measured	Subtracted	4567.04	5631.2	1064.16	
314	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Squared	Divided	71576.8	56326.7	1.27074	
314	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Rooted	Subtracted	59.6399	51.9242	7.7157	
314	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Ranked	Subtracted	88.2482	110.265	22.0168	

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/