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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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

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/