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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Gene Rank description Network Comparison Type Value Type Interaction Map Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 501 to 550 of 29840 in total
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Value Type
Filtered
green
network_comparison
red
32 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Subtracted Ranked 1 336.074 68.932 267.142
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided Measured 895.893 2.04793 1834.73
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted Rooted 0 9.43398 9.43398 0
importin 9. [refseq;acc:nm_018085] Divided Ranked 8691.76 1.52929 13292.2
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Subtracted Measured 1 18263 5430.7 23693.7
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 58 801 859
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Squared 1 192141 85915 106226
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Divided 0 4.57302 16.8159 76.8994
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Ranked 1 243.673 1.29985 187.462
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Subtracted Squared 0 27221.2 7328.6 19892.6
syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked 19014.6 5130.2 13884.4
ubiquitin protein ligase. [refseq;acc:nm_130466] Divided Rooted 11.258 2.13529 24.0391
33 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Subtracted Squared 36822.7 7010.7 29812
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Divided 4.57302 16.8159 76.8994
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Rooted 25.7294 2.0801 12.3693
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Subtracted Ranked 1 336.073 68.929 267.144
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided Measured 896.972 2.04611 1835.3
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 0 39.8063 3.15402 12.6208
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted 1 18263 5430.7 23693.7
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Rooted 0 70.9983 9.359 61.6393
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Divided Ranked 8691.76 1.52929 13292.2
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Subtracted Squared 1 192141 85915 106226
protein cgi-147. [swissprot;acc:q9y3e5] Measured 0 9192.38 796.26 8396.12
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Rooted 1 43.561 17.8623 25.6987
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Divided 43.1914 1.65937 26.0288
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Ranked 242.742 1.28647 188.688
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Subtracted 0 20387 5123 15264
spermatogenesis associated 6. [refseq;acc:nm_019073] Divided Squared 1 25146.6 2.53372 9924.76
34 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Subtracted Measured 0 3340.03 791.03 4131.06
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Divided Squared 1 25146.6 2.53372 9924.76
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Subtracted 0 72701 6682.4 79383.4
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Ranked 6812 4731 11543
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Rooted 1 122.878 17.63 140.508
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Divided Measured 0 47 3.04255 143
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Subtracted Ranked 1 336.073 68.929 267.144
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided Measured 907.546 2.02382 1836.71
Rooted 24.3678 1.65305 40.2812
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Squared 0 0.697197 15.9968 0.0435834
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Subtracted Measured 1 18263 5430.7 23693.7
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Divided Ranked 0 17173.8 1.52196 11284
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Subtracted Squared 1 192141 85915 106226
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Divided Rooted 0 11.7898 2.02503 23.8747
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Ranked 1 242.453 1.28235 189.07
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Subtracted Rooted 0 12.49 9.32772 3.16228
35 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided Squared 1 192141 1.80879 106226
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Measured 0 1377 2.99674 459.5
Squared 647.816 12.7767 50.7031
apg3p; pc3-96 protein. [refseq;acc:nm_022488] Subtracted Rooted 1 122.878 17.63 140.508
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Divided 0 11.7898 2.02503 23.8747
bystin. [swissprot;acc:q13895] Subtracted Squared 32857.7 6288 26569.7

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/