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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Value Type Gene Network Comparison Type description Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 29840 in total
Interaction Map  : High confidence
Rank
Value Type
Network Comparison Type
description
red
Filtered
green
network_comparison
32 Ranked Divided importin 9. [refseq;acc:nm_018085] 13292.2 0 8691.76 1.52929
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] 187.462 1 243.673 1.29985
Subtracted guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 267.142 336.074 68.932
syntaxin 10 (syn10). [swissprot;acc:o60499] 13884.4 0 19014.6 5130.2
Squared Divided beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 9924.76 1 25146.6 2.53372
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 76.8994 0 4.57302 16.8159
Subtracted pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 106226 1 192141 85915
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] 19892.6 0 27221.2 7328.6
Rooted Divided ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 26.0288 1 43.1914 1.65937
ubiquitin protein ligase. [refseq;acc:nm_130466] 24.0391 0 11.258 2.13529
Subtracted gbp protein isoform a. [refseq;acc:nm_017870] 23.9771 1 42.4773 18.5002
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 0 9.43398 9.43398
33 Measured Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 1835.3 1 896.972 2.04611
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 12.6208 0 39.8063 3.15402
Subtracted melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 23693.7 1 18263 5430.7
protein cgi-147. [swissprot;acc:q9y3e5] 8396.12 0 9192.38 796.26
Ranked Divided nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 13292.2 8691.76 1.52929
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] 188.688 1 242.742 1.28647
Subtracted guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] 267.144 336.073 68.929
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 15264 0 20387 5123
Squared Divided beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 76.8994 4.57302 16.8159
spermatogenesis associated 6. [refseq;acc:nm_019073] 9924.76 1 25146.6 2.53372
Subtracted ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 29812 0 36822.7 7010.7
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 106226 1 192141 85915
Rooted Divided fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 12.3693 0 25.7294 2.0801
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 26.0288 1 43.1914 1.65937
Subtracted nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 61.6393 0 70.9983 9.359
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 25.6987 1 43.561 17.8623
34 Measured Divided glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 143 0 47 3.04255
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 1836.71 1 907.546 2.02382
Subtracted acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 4131.06 0 3340.03 791.03
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 23693.7 1 18263 5430.7
Ranked Divided microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 11284 0 17173.8 1.52196
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] 189.07 1 242.453 1.28235
Subtracted fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 11543 0 6812 4731
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] 267.144 1 336.073 68.929
Squared Divided amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 9924.76 25146.6 2.53372
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 0.0435834 0 0.697197 15.9968
Subtracted coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 79383.4 72701 6682.4
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 106226 1 192141 85915
Rooted Divided guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 40.2812 24.3678 1.65305
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 23.8747 0 11.7898 2.02503
Subtracted gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 140.508 1 122.878 17.63
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] 3.16228 0 12.49 9.32772
35 Measured Divided adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 459.5 1377 2.99674
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 1836.71 1 907.564 2.02378
Subtracted filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 1603 0 898 705
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 23693.7 1 18263 5430.7
Ranked Divided nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 3208.8 0 4871.6 1.5182
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 260.532 1 204.309 1.27519

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/