MK5 Microarray Data

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

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	Value Type	Hugo	description	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 680 to 729 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	Hugo	description	red	green	network_comparison
170	Rooted	B9D1	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	53.4993	45.9227	1.16499
171	Measured	MAGED2	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	23693.7	18263	1.29736
	Ranked	TIAL1	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	227.202	192.823	1.17829
	Squared	CTPS	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	96602.7	69211.2	1.39577
	Rooted	LASS2	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	61.6639	71.7355	1.16333
172	Measured	TRO	trophinin. [swissprot;acc:q12816]	23693.7	18263	1.29736
	Ranked	TIPRL	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	174.667	205.556	1.17685
	Squared	CSTF2T	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	121579	87259.3	1.39331
	Rooted	SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	56.7592	65.9889	1.16261
173	Measured	BCAR3	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	4579.34	5940.64	1.29727
	Ranked	SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	227.032	193.056	1.17599
	Squared	SEPT4	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]	82624.3	115061	1.39258
	Rooted	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	145.551	168.796	1.1597
174	Measured	MXD1	mad protein (max dimerizer). [swissprot;acc:q05195]	4455.95	5774.03	1.2958
	Ranked	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	335	286	1.17133
	Squared	ZNF547	sedlin. [swissprot;acc:o14582]	112820	157033	1.39189
	Rooted	PANK1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	145.551	168.796	1.1597
175	Measured	MXI1	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	4456.67	5773.77	1.29553
	Ranked	COPS3	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	199.949	234.187	1.17123
	Squared	no value	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	112820	157033	1.39189
	Rooted	PANK2	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	145.551	168.796	1.1597
176	Measured	MXD4	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	4456.93	5773.67	1.29544
	Ranked	POLE4	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	275.754	235.908	1.1689
	Squared	TRAPPC3	bet3 homolog. [swissprot;acc:o43617]	112820	157033	1.39189
	Rooted	PANK3	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	145.551	168.796	1.1597
177	Measured	RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	4457.06	5773.63	1.29539
	Ranked	NCBP2L	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	229.406	196.695	1.1663
	Squared	SEPT1	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	78383	108483	1.38401
	Rooted	SLC25A43	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	145.551	168.796	1.1597
178	Measured	MYO5B	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	21591.5	27904.5	1.29238
	Ranked	no value	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	226.887	194.72	1.1652
	Squared	CPA6	carboxypeptidase b precursor. [refseq;acc:nm_020361]	25326.4	18354.1	1.37988
	Rooted	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	45.7414	52.932	1.1572
179	Measured	MYO5C	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	21591.5	27904.5	1.29238
	Ranked	no value	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	226.884	194.79	1.16476
	Squared	CPA3	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	25326.3	18354.1	1.37987
	Rooted	EGFL8	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	50.272	43.4634	1.15665
180	Measured	no value	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	21591.5	27904.5	1.29238
	Ranked	TARDBP	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	256.228	298.438	1.16474
	Squared	CPB2	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	25326.2	18354.1	1.37987
	Rooted	EGFL7	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	50.2801	43.4779	1.15645
181	Measured	EIF4G3	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	4068.56	5252.6	1.29102
	Ranked	B9D1	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	229.818	267.265	1.16294
	Squared	NFU1	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	55630.4	76083.7	1.36766
	Rooted	BCAR1	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	57.4432	66.3307	1.15472
182	Measured	no value	rna-binding protein. [refseq;acc:nm_019027]	4069.83	5252.17	1.29051
	Ranked	HAT1	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	277.546	240.461	1.15422
	Squared	DUT	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316]	61733.5	45224.1	1.36506
	Rooted	CCT4	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	57.45	66.332	1.1546
183	Measured	no value	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	4069.83	5252.17	1.29051

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
- Hugo is the HGNC identifier if it exists
- 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.