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 Value Type description Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 375 to 424 of 12912 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
94 Squared ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 84857.8 53402.4 1.58903
Rooted chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 47.6504 36.9304 1.29028
95 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
Ranked melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 88.2482 110.265 1.24949
Squared protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 256169 162517 1.57626
Rooted regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 47.6504 36.9304 1.29028
96 Measured lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 4110.14 5694.99 1.3856
Ranked melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 88.2482 110.265 1.24949
Squared atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 7744.68 4959.41 1.56161
Rooted putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 47.6504 36.9304 1.29028
97 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] 2820.51 3897.1 1.3817
Ranked melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 88.2482 110.265 1.24949
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] 227160 146079 1.55505
Rooted regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] 47.6504 36.9304 1.29028
98 Measured presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 2353.63 3225.65 1.3705
Ranked melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 88.2482 110.265 1.24949
Squared trs85 homolog. [swissprot;acc:q9y2l5] 227160 146079 1.55505
Rooted transcription factor lbx1. [swissprot;acc:p52954] 47.6504 36.9304 1.29028
99 Measured s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] 2353.63 3225.65 1.3705
Ranked melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 88.2482 110.265 1.24949
Squared wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 226186 145568 1.55382
Rooted mosaic protein lgn. [swissprot;acc:p81274] 47.6504 36.9304 1.29028
100 Measured f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 2353.63 3225.65 1.3705
Ranked melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 88.2482 110.265 1.24949
Squared cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 226186 145568 1.55382
Rooted regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 47.6504 36.9304 1.29028
101 Measured cullin homolog 2 (cul-2). [swissprot;acc:q13617] 2353.63 3225.65 1.3705
Ranked melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 88.2482 110.265 1.24949
Squared cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 222655 143584 1.5507
Rooted guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 47.6504 36.9304 1.29028
102 Measured presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 2353.63 3225.65 1.3705
Ranked 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] 88.2482 110.265 1.24949
Squared fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 214143 138337 1.54798
Rooted rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 47.6504 36.9304 1.29028
103 Measured cullin homolog 1 (cul-1). [swissprot;acc:q13616] 2353.63 3225.65 1.3705
Ranked trophinin. [swissprot;acc:q12816] 88.2482 110.265 1.24949
Squared mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 407289 263351 1.54656
Rooted proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 60.8365 77.7233 1.27758
104 Measured musashi 2 isoform a. [refseq;acc:nm_138962] 4241.57 5810.79 1.36996
Ranked homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 252.371 202.016 1.24926
Squared cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 407289 263351 1.54656
Rooted jun dimerization protein. [refseq;acc:nm_130469] 60.8365 77.7233 1.27758
105 Measured musashi 1. [refseq;acc:nm_002442] 4241.57 5810.79 1.36996
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 266.716 333.165 1.24914
Squared cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 407289 263351 1.54656
Rooted fos-related antigen 2. [swissprot;acc:p15408] 60.8675 77.7168 1.27682
106 Measured nuclear protein ukp68. [refseq;acc:nm_024824] 4241.57 5810.79 1.36996
Ranked ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 252.329 202.004 1.24913
Squared cytohesin 4. [swissprot;acc:q9uia0] 407289 263351 1.54656
Rooted protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 60.8692 77.7165 1.27678

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/