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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Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 723 to 772 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
91 GNA11 Rooted guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Subtracted 40.2812 24.3678 15.9134
HRAS Measured transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 16070.4 12886 3184.4
KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 2416.53 1700.8 1.42082
LBX1 Ranked transcription factor lbx1. [swissprot;acc:p52954] Subtracted 249.663 298.263 48.6
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Divided 88.2482 110.265 1.24949
RALGDS Squared ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 90432.9 56304.2 1.60615
92 no value Measured transforming protein n-ras. [swissprot;acc:p01111] Subtracted 16069.8 12885.6 3184.2
GNAQ Rooted guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 40.2812 24.3679 15.9133
GPSM2 Ranked mosaic protein lgn. [swissprot;acc:p81274] 249.663 298.263 48.6
HRAS Squared transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 105473 64132.3 41340.7
MAGEF1 Ranked melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 88.2482 110.265 1.24949
NCBP2L Measured dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 4117.67 5801.04 1.40882
PITRM1 Squared metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 29570.7 18601.8 1.58967
PSEN1 Rooted presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 37.3005 48.4141 1.29795
93 no value Measured formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 4245.52 5942.75 1.39977
Squared transforming protein n-ras. [swissprot;acc:p01111] Subtracted 105469 64130.2 41338.8
ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Divided 29567 18601.6 1.58949
CUL1 Rooted cullin homolog 1 (cul-1). [swissprot;acc:q13616] 37.3005 48.4141 1.29795
GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Subtracted 40.2805 24.369 15.9115
MAGEB6B Ranked melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided 88.2482 110.265 1.24949
RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Subtracted 249.663 298.263 48.6
ZNF547 Measured sedlin. [swissprot;acc:o14582] 17396.9 20483.9 3087
94 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 4247.86 5941.88 1.39879
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Subtracted 17396.9 20483.9 3087
Ranked melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 88.2482 110.265 1.24949
GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Subtracted 249.663 298.263 48.6
GNAT1 Rooted guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 40.2805 24.3691 15.9114
PPP1R13B Squared protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 124319 86848.2 37470.8
RBM15B Rooted chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Divided 47.6504 36.9304 1.29028
RGL1 Squared ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 84857.8 53402.4 1.58903
95 GNAT2 Rooted guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Subtracted 40.2804 24.3692 15.9112
MAGEA9 Ranked melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Divided 88.2482 110.265 1.24949
PPP1R7 Squared protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 256169 162517 1.57626
RAP1GAP Ranked rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Subtracted 249.663 298.263 48.6
RGS19 Rooted regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Divided 47.6504 36.9304 1.29028
SON Measured 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] 2397.19 3343.62 1.39481
TP53BP2 Squared tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Subtracted 123324 86277.9 37046.1
TRAPPC3 Measured bet3 homolog. [swissprot;acc:o43617] 17396.9 20483.9 3087
96 no value Squared atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Divided 7744.68 4959.41 1.56161
ATF3 Ranked cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Subtracted 201.949 153.671 48.278
GNAI2 Rooted guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 40.28 24.37 15.91
LASS2 Measured lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided 4110.14 5694.99 1.3856
MAGEA8 Ranked melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 88.2482 110.265 1.24949
RBM15 Rooted putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 47.6504 36.9304 1.29028
SEPT8 Measured septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted 16177.9 19235.4 3057.5
Squared 90226 126939 36713
97 APBA1 Measured amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Divided 2820.51 3897.1 1.3817
Ranked Subtracted 271.752 225.68 46.072
CPSF4 Squared cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Divided 227160 146079 1.55505
CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted 126408 89940.5 36467.5

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/