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.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 3180 to 3229 of 77072 in total

Rank	Network Comparison Type	description	Filtered	Value Type	Interaction Map	network_comparison	red	green
100	Divided	set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197]	1	Measured	Low confidence	1.10037	5752.65	6330.03
		transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	0	Rooted		1.29099	5.47723	7.07107
		transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	0	Measured		1.48306	817.81	551.434
		tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881]	1	Squared		1.17533	70019.5	82296.2
		zinc finger protein 277. [swissprot;acc:q9nrm2]	0	Ranked		1.2179	8725.56	10626.9
	Subtracted	b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251]	1	Ranked		14.818	200.497	185.679
		ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	0	Rooted	High confidence	4.7958	22.4608	17.665
		cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	1	Measured	Low confidence	939.7	12375.5	11435.8
		dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	0	Measured	High confidence	311.6	2698.62	3010.22
		dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	0	Ranked		2113.9	12584.5	10470.6
		fos-related antigen 2. [swissprot;acc:p15408]	1	Ranked		43.595	204.641	161.046
		hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	0	Squared	Low confidence	2761.4	16325.5	13564.1
		high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	0		High confidence	1372	310373	311745
		monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021]	1		Low confidence	8887.6	63904	72791.6
		putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	0	Ranked	Low confidence	2139.8	11725.7	13865.5
		septin 6. [swissprot;acc:q14141]	1	Measured	High confidence	2997.2	15959.9	18957.1
		septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]		Squared		36046.2	89182.8	125229
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]		Rooted		15.8355	19.9625	35.798
		transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]		Rooted	Low confidence	6.2355	61.9982	68.2337
		zinc finger protein 117 (zinc finger protein hpf9) (fragment). [swissprot;acc:q03924]	0	Measured		382.99	2352.42	1969.43
		zinc finger protein 84 (zinc finger protein hpf2). [swissprot;acc:p51523]		Rooted		4.593	45.3043	40.7113
101	Divided	60s ribosomal protein l37a. [swissprot;acc:p12751]		Measured		1.47569	535.61	362.955
		b24o18.3 (pom121 membrane glycoprotein (rat homolog)-like 2). [sptrembl;acc:q96kw2]		Squared		2.12849	27.0961	12.7302
		cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	1	Squared	High confidence	1.5507	222655	143584
		cullin homolog 2 (cul-2). [swissprot;acc:q13617]	1	Measured		1.3705	2353.63	3225.65
		dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	0	Ranked		1.221	14548.5	11915.2
		dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	0	Rooted	Low confidence	1.28861	13.7191	17.6786
		guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]	1	Rooted	High confidence	1.29028	47.6504	36.9304
		leucine zipper domain protein. [refseq;acc:nm_024589]	1	Ranked	Low confidence	1.07579	221.996	238.82
		low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	0	Rooted	High confidence	1.30182	12.6886	9.74679
		melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	1	Ranked		1.24949	88.2482	110.265
		putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	0	Measured		1.47595	1442	977
		raptor; p150 target of rapamycin (tor)-scaffold protein containing wd-repeats. [refseq;acc:nm_020761]	1	Squared	Low confidence	1.16811	63526.9	54384.3
		set and mynd domain containing protein 1. [sptrembl;acc:q8nb12]	1	Measured		1.10037	5752.65	6330.03
		similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	0	Ranked		1.21766	8703.84	10598.3
		transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	0	Squared	High confidence	2.16725	956.375	441.285
		vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]	1	Rooted	Low confidence	1.08881	69.1897	75.3346
	Subtracted	coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488]	1	Ranked	Low confidence	14.682	226.395	211.713
		coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	0	Ranked	High confidence	2084.3	12577.8	14662.1
		dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	1	Rooted		15.8355	19.9625	35.798
		e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	0	Rooted		4.7716	34.3021	29.5305
		ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]		Squared		1328.42	5294.83	3966.41
		formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]		Measured		308.673	638.862	330.189
		kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]		Ranked	Low confidence	2106.51	7923.89	10030.4
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	1	Measured	Low confidence	927.4	10685.5	11612.9
		protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]		Ranked	High confidence	43.59	204.641	161.051
		segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]		Rooted	Low confidence	6.1956	68.4921	74.6877
		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). [swissprot;acc:o43236]		Measured	High confidence	2730.8	14924.4	17655.2
		septin 6. [swissprot;acc:q14141]		Squared	High confidence	35900.4	88953.6	124854
		solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593]		Squared	Low confidence	8887.1	63903.1	72790.2

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/