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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 718 to 767 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
90	necdin. [swissprot;acc:q99608]	Ranked	1	88.2482	110.265	1.24949
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	Measured		2414.77	1698.75	1.4215
	transforming protein n-ras. [swissprot;acc:p01111]	Squared		105469	64130.2	1.64461
91	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	Ranked	0	13841.2	11127.5	1.24387
	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Rooted	1	37.3005	48.4141	1.29795
	lats homolog 1. [refseq;acc:nm_004690]	Squared	0	12.5892	5.42219	2.32179
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Ranked	1	88.2482	110.265	1.24949
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Measured	1	2416.53	1700.8	1.42082
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Measured	0	39.7924	62.2106	1.56338
	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	Squared	1	90432.9	56304.2	1.60615
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Rooted	0	11.5003	8.68906	1.32354
92	adp-ribosylation factor 3. [swissprot;acc:p16587]	Measured	0	300.697	469.346	1.56086
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Measured	1	4117.67	5801.04	1.40882
	dok-like protein. [refseq;acc:nm_024872]	Ranked	0	17571	21783	1.23971
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Rooted	0	25.1701	33.2721	1.32189
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Ranked	1	88.2482	110.265	1.24949
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Squared		29570.7	18601.8	1.58967
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Rooted		37.3005	48.4141	1.29795
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	Squared	0	12.5892	5.42219	2.32179
93	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Squared	1	29567	18601.6	1.58949
	cab2. [refseq;acc:nm_033419]	Rooted	0	0.00001	13.1909	1319090
	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	Rooted	1	37.3005	48.4141	1.29795
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Measured	0	528.5	816.5	1.54494
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Measured	1	4245.52	5942.75	1.39977
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Ranked	1	88.2482	110.265	1.24949
	myosin vi. [swissprot;acc:q9um54]	Squared	0	39.56	17.2035	2.29953
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Ranked		7739.47	9580.95	1.23793
94	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Squared		122.543	53.9854	2.26993
	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Rooted	1	47.6504	36.9304	1.29028
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	Rooted	0	24.7769	18.7862	1.31889
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Measured	1	4247.86	5941.88	1.39879
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Ranked	1	88.2482	110.265	1.24949
	myosin vi. [swissprot;acc:q9um54]	Measured	0	345.865	224.096	1.54338
	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	Squared	1	84857.8	53402.4	1.58903
	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	Ranked	0	12946.3	10519.7	1.23067
95	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Ranked	1	88.2482	110.265	1.24949
	metaxin 1. [swissprot;acc:q13505]	Rooted	0	14.7289	11.2174	1.31304
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Measured		154	0.00001	15400000
	pp3111 protein. [refseq;acc:nm_022156]	Ranked		6185	7603	1.22926
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared	1	256169	162517	1.57626
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Rooted		47.6504	36.9304	1.29028
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Measured		2397.19	3343.62	1.39481
	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	Squared	0	631.532	280.389	2.25234
96	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		1	7744.68	4959.41	1.56161
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]		0	52.0821	116.513	2.2371
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Ranked	0	8335.82	10228.3	1.22703
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Measured	1	4110.14	5694.99	1.3856
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Ranked		88.2482	110.265	1.24949
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Rooted		47.6504	36.9304	1.29028
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Measured	0	154	0.00001	15400000

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/