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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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 Rank Gene description Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1158 to 1207 of 29840 in total

Value Type

: Measured
Interaction Map

: High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison
290	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Subtracted	1	4071.1	5251.75	1180.65
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	0	0	89	89
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Divided	1	4991.48	6014.08	1.20487
291	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Subtracted	0	0	89	89
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Subtracted	1	5894.75	7073.65	1178.9
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	1	44490.5	36927.5	1.20481
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]		0	1961.09	2179.77	1.11151
292	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]		0	11223	12473	1.11138
	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]		1	4641.09	5588.75	1.20419
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Subtracted	1	950.561	2108.52	1157.96
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]		0	952.488	863.886	88.602
293	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]			764.479	676.971	87.508
	block 23. [sptrembl;acc:q8nhw5]	Divided		1943.32	2159.55	1.11127
	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Divided	1	4641.09	5588.75	1.20419
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [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. [refseq;acc:nm_001326]	Divided		22515.5	18702.6	1.20387
	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	Subtracted	0	841.301	753.849	87.452
	mesoderm induction early response 1. [refseq;acc:nm_020948]	Divided	0	1914.5	1723.5	1.11082
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Subtracted	1	4512.19	5655.52	1143.33
295	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	Divided	0	426.8	384.843	1.10902
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Subtracted	1	5720.25	4577.5	1142.75
	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	Divided	1	13261.9	11017.8	1.20368
	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	Subtracted	0	717.401	804.725	87.324
296	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]		0	2131.42	2218.51	87.09
	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). [swissprot;acc:q13952]		1	3620.77	4763.34	1142.57
	pnas-18. [sptrembl;acc:q9bzu3]	Divided	0	2256.05	2035.28	1.10847
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]		1	4911.81	5909.18	1.20306
297	40s ribosomal protein s29. [swissprot;acc:p30054]		0	1711.6	1895.38	1.10737
	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Subtracted	1	3620.77	4763.34	1142.57
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Subtracted	0	2131.52	2218.58	87.06
	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). [swissprot;acc:q13887]	Divided	1	4911.81	5909.18	1.20306
298	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109]	Subtracted	1	8268.19	9405.85	1137.66
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Subtracted	0	2131.83	2218.82	86.99
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Divided	1	4633.92	5572.85	1.20262
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]		0	939	848	1.10731
299	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		1	4914.27	5907.12	1.20203
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]		0	2231.05	2015.09	1.10717
	histone h2b. [refseq;acc:nm_175055]	Subtracted	0	2131.91	2218.89	86.98
	metaxin 1. [swissprot;acc:q13505]		1	9327.58	10442.2	1114.62
300	histone h2b.e (h2b/e). [swissprot;acc:q99879]		0	2131.93	2218.9	86.97
	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	Divided	0	1334.19	1205.1	1.10712
	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). [swissprot;acc:q92994]	Subtracted	1	4446.72	5553.79	1107.07
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	Divided		4914.27	5907.12	1.20203
301	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]			13768.2	11466	1.20078
	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]		0	135.294	149.371	1.10405
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Subtracted	0	2132.04	2218.98	86.94
	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	Subtracted	1	4446.72	5553.79	1107.07
302	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Divided	0	135.294	149.371	1.10405
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Divided	1	5894.75	7073.65	1.19999
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Subtracted	1	6704.44	7811.45	1107.01

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/