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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

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Showing element 51 to 100 of 3228 in total

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

Rank	description	Hugo	red	green	network_comparison
51	spermatogenesis associated 6. [refseq;acc:nm_019073]	SPATA6	133	105	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	AMPD2
53	transcription factor jun-b. [swissprot;acc:p17275]	JUNB	201.144	158.868	1.26611
54	transcription factor jun-d. [swissprot;acc:p17535]	JUND	200.941	158.941	1.26425
55	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	PRKRAP1	320.927	254.434	1.26134
56	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	no value	266.856	336.233	1.25998
57	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	GNG12
58	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	GNG4	266.863	336.191	1.25979
59	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	GNG3		336.19	1.25978
60	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	GNG8	266.864	336.184	1.25976
61	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	GNG5		336.182	1.25975
62	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	GNG10	266.865	336.181	1.25974
63	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	no value		336.178	1.25973
64	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	GNG11	266.868	336.159	1.25965
65	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	GNAQ	267.136	336.077	1.25807
66	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	GNA11
67	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	GNAT2	267.14	336.075	1.25805
68	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	GNAZ	267.139
69	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	GNAT1	267.14
70	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	GNAI2	267.142	336.074	1.25804
71	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	GNAI1	267.144	336.073	1.25802
72	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	GNAI3
73	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	JPH3	288	362	1.25694
74	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	JPH2
75	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	SMPD2
76	db83 protein. [swissprot;acc:p57088]	TMEM33
77	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	CACNG2	254.692	202.668	1.2567
78	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	CACNG8	254.693
79	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	CACNG3
80	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	CACNG4	254.691		1.25669
81	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	CACNG5	254.614	202.646	1.25645
82	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	GNB5	267.636	335.359	1.25304
83	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	MAGED4	88.2482	110.265	1.24949
84	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	MAGEE2
85	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	no value
86	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	MAGEA11
87	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	MAGEA2B
88	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	no value
89	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	MAGEA6
90	necdin. [swissprot;acc:q99608]	NDN
91	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	MAGED1
92	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	MAGEF1
93	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	MAGEB6B
94	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	no value
95	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	MAGEA9
96	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	MAGEA8
97	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	MAGEC1
98	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	MAGEA4
99	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	no value
100	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	MAGEA10

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.