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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 583 to 632 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
292	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Divided	4641.09	5588.75	1.20419	
292	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Subtracted	950.561	2108.52	1157.96	
293	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Divided	4641.09	5588.75	1.20419	
293	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Subtracted	4512.19	5655.52	1143.33	
294	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Divided	22515.5	18702.6	1.20387	
294	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Subtracted	4512.19	5655.52	1143.33	
295	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Subtracted	5720.25	4577.5	1142.75	
295	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [source:swissprot;acc:q9nzl6]	Divided	13261.9	11017.8	1.20368	
296	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Subtracted	3620.77	4763.34	1142.57	
296	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	Divided	4911.81	5909.18	1.20306	
297	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Subtracted	3620.77	4763.34	1142.57	
297	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887]	Divided	4911.81	5909.18	1.20306	
298	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Subtracted	8268.19	9405.85	1137.66	
298	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]	Divided	4633.92	5572.85	1.20262	
299	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Divided	4914.27	5907.12	1.20203	
299	metaxin 1. [source:swissprot;acc:q13505]	Subtracted	9327.58	10442.2	1114.62	
300	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	Subtracted	4446.72	5553.79	1107.07	
300	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Divided	4914.27	5907.12	1.20203	
301	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	Divided	13768.2	11466	1.20078	
301	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Subtracted	4446.72	5553.79	1107.07	
302	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	Divided	5894.75	7073.65	1.19999	
302	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Subtracted	6704.44	7811.45	1107.01	
303	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [source:swissprot;acc:p36873]	Divided	22268.8	18560.4	1.1998	
303	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Subtracted	4723.53	5828.46	1104.93	
304	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Subtracted	5221.28	6314.35	1093.07	
304	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	Divided	4855.46	5824.52	1.19958	
305	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Divided	3856.29	4624.15	1.19912	
305	paxillin. [source:swissprot;acc:p49023]	Subtracted	5221.28	6314.35	1093.07	
306	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	Subtracted	8430.03	9518.11	1088.08	
306	pnas-18. [source:sptrembl;acc:q9bzu3]	Divided	13680.5	11409.6	1.19903	
307	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [source:swissprot;acc:o15120]	Subtracted	7556.75	8636.87	1080.12	
307	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	Divided	12365.2	14824.9	1.19892	
308	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	Subtracted	11852.9	10773.5	1079.4	
308	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	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]	Subtracted	11848.8	10770.3	1078.5	
309	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Divided	4977.8	5966.14	1.19855	
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]	Subtracted	7551.8	8630.06	1078.26	
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]	Divided	4909.79	5878.79	1.19736	
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]	Subtracted	2820.51	3897.1	1076.59	
311	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Divided	4981.52	5964.58	1.19734	
312	max protein. [source:swissprot;acc:p25912]	Subtracted	4640.26	5704.87	1064.61	
312	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Divided	4598.21	5500.48	1.19622	
313	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Divided	21644.2	18098.7	1.1959	
313	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Subtracted	4567.04	5631.2	1064.16	
314	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Subtracted	6563.65	7627.29	1063.64	
314	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Divided	21632.5	18090	1.19583	
315	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Divided	21370.8	17896.5	1.19413	
315	vav proto-oncogene. [source:swissprot;acc:p15498]	Subtracted	6644.99	7707.8	1062.81	
316	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Divided	21370.8	17896.5	1.19413	
316	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	Subtracted	6603.41	7664.65	1061.24	

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/