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

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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description Rank Network Comparison Type Gene Hugo Interaction Map Value Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 308 to 357 of 473 in total
Network Comparison Type  : Subtracted
Interaction Map  : High confidence
Value Type  : Ranked
Filtered  : 1
red  : 0
green  : 0
network_comparison  : 0
description
Rank
Hugo
ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907] 2764 RAB11B
ras-related protein rab-1a (ypt1-related protein). [swissprot;acc:p11476] 2961 RAB1A
ras-related protein rab-1b. [swissprot;acc:q9h0u4] 2807 RAB1C
ras-related protein rab-2a. [swissprot;acc:p08886] 3110 RAB2A
ras-related protein ral-a. [swissprot;acc:p11233] 3223 RALA
ras-related protein ral-b. [swissprot;acc:p11234] 2925 RALB
rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781] 3205 RB1CC1
rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [refseq;acc:nm_005444] 2924 RQCD1
recessive polycystic kidney disease protein tg737 homolog. [swissprot;acc:q13099] 3201 IFT88
regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [swissprot;acc:q15714] 3114 TSC22D1
retinoic acid receptor rxr-alpha. [swissprot;acc:p19793] 2759 RXRA
retinoic acid receptor rxr-beta. [swissprot;acc:p28702] 3067 no value
retinoic acid receptor rxr-gamma. [swissprot;acc:p48443] 2936 RXRG
ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [swissprot;acc:q9nrr4] 3059 RNASEN
ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329] 2916 PRPS1L1
ribose-phosphate pyrophosphokinase ii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase ii) (ppribp) (prs-ii). [swissprot;acc:p11908] 3122 PRPS2
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 2895 no value
ring finger protein 3. [refseq;acc:nm_006315] 2763 PCGF3
ring finger protein 4. [swissprot;acc:p78317] 3189 RNF4
rna-binding protein 8a (rna binding motif protein 8a) (ribonucleoprotein rbm8a) (rna-binding protein y14) (binder of ovca1- 1) (bov-1). [swissprot;acc:q9y5s9] 2996 RBM8A
rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640] 3198 DCUN1D1
runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196] 2877 RUNX1
runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761] 3208 RUNX3
rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] 3073 RWDD1
sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3] 3124 SAMHD1
schwannomin interacting protein 1. [refseq;acc:nm_014575] 2900 SCHIP1
sec23-interacting protein p125; phospholipase. [refseq;acc:nm_007190] 3097 SEC23IP
semaphorin 6b precursor (semaphorin z) (sema z). [swissprot;acc:q9h3t3] 2832 SEMA6B
semaphorin 6c precursor (semaphorin y) (sema y). [swissprot;acc:q9h3t2] 2933 SEMA6C
semaphorin 6d isoform 3 precursor. [refseq;acc:nm_153617] 2964 SEMA6D
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] 2843 SENP8
serine/threonine kinase 38 like. [refseq;acc:nm_015000] 2897 no value
serine/threonine kinase 38; serine threonine protein kinase. [refseq;acc:nm_007271] 3071 STK38
serine/threonine protein kinase 24 (ec 2.7.1.37) (ste20-like kinase mst3) (mst-3) (mammalian ste20-like protein kinase 3). [swissprot;acc:q9y6e0] 3115 STK24
serine/threonine protein kinase 25 (ec 2.7.1.37) (sterile 20/oxidant stress-response kinase 1) (ste20/oxidant stress response kinase-1) (sok-1) (ste20-like kinase). [swissprot;acc:o00506] 3048 STK25
serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [swissprot;acc:q13188] 3111 STK3
serine/threonine protein kinase mask; ste20-like kinase mst4. [refseq;acc:nm_016542] 2982 no value
serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757] 2908 CHEK1
serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] 3137 CDKL1
serine/threonine-protein kinase receptor r3 precursor (ec 2.7.1.37) (skr3) (activin receptor-like kinase 1) (alk-1) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:p37023] 2952 ACVRL1
set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105] 3039 SET
sex comb on midleg homolog 1. [refseq;acc:nm_012236] 3217 SCMH1
sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089] 3120 SCML2
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] 2794 SH2B1
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] 2867 no value
similar to cg5057 gene product. [sptrembl;acc:q9btt4] 2984 MED10
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 3032 LYZL1
similar to mob-lak. [refseq;acc:nm_145279] 2937 MOBKL2C
skd1 protein (vacuolar sorting protein 4b). [swissprot;acc:o75351] 3037 VPS4B
skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [refseq;acc:nm_016532] 2994 no value

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.
- http://analysis.yellowcouch.org/