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 493 to 542 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
124 HMG20B Ranked high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 208.52 171.595 1.21519
MAP1LC3B Measured microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 24255.7 18168.9 1.33501
PPP1R2P9 Squared type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 192779 126095 1.52884
TIAL1 Rooted nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 54.6625 67.9477 1.24304
125 HMG20A Ranked high-mobility group 20a. [refseq;acc:nm_018200] 208.588 171.778 1.21429
MAP1LC3A Measured microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 24255.7 18168.9 1.33501
RRS1 Squared ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 189976 124480 1.52616
SNRPD1 Rooted small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 54.8203 67.934 1.23921
126 ATG4B Measured cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 24250 18164.9 1.33499
HMG20B Rooted high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 60.9342 75.1387 1.23311
PPP1CA Squared serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 189976 124480 1.52616
STAMBPL1 Ranked associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 94 114 1.21277
127 no value Squared cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 88432.6 58423.3 1.51365
CHMP2A Ranked putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 94 114 1.21277
HMG20A Rooted high-mobility group 20a. [refseq;acc:nm_018200] 60.9353 75.094 1.23236
JUND Measured transcription factor jun-d. [swissprot;acc:p17535] 5638.2 7523.39 1.33436
128 no value Squared pnas-18. [sptrembl;acc:q9bzu3] 87787.3 58155.8 1.50952
LUC7L2 Measured luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 4355.61 5810.82 1.3341
STAMBP Ranked associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 94 114 1.21277
TARDBP Rooted tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 48.0515 39.0445 1.23069
129 LUC7L Measured luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 4358.13 5811.49 1.33348
NCBP2L Rooted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 54.2343 66.7323 1.23044
PCF11 Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 178263 118639 1.50257
VPS24 Ranked neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 94 114 1.21277
130 no value Rooted formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 55.1026 67.5701 1.22626
C10orf83 Squared 44050 protein. [refseq;acc:nm_178832] 148058 99628.4 1.4861
CHMP4A Ranked protein hspc134 (protein cda04). [swissprot;acc:q9by43] 94 114 1.21277
FOXP4 Measured forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 2234.68 2978.53 1.33287
131 no value Rooted huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 55.1113 67.5537 1.22577
FOXP1 Measured forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 2234.73 2978.57 1.33285
PPP1R8 Squared nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] 148058 99628.4 1.4861
SON Ranked 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] 294.053 242.562 1.21228
132 ATG5 Squared autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 36359.2 24466.8 1.48606
FOXP3 Measured forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 2236.61 2980.35 1.33253
HAT1 Rooted histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 44.963 55.0576 1.22451
TOB2 Ranked tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 350 290 1.2069
133 GABARAP Measured gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 23421.5 17580.4 1.33225
OSR1 Rooted odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 45.4558 55.5995 1.22316
TMEM132A Squared gbp protein isoform a. [refseq;acc:nm_017870] 1182.25 1726.55 1.46039
TOB1 Ranked tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 350 290 1.2069
134 no value Measured gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 21785.2 16426.1 1.32626
DAB2IP Ranked dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 350 290 1.2069
GATAD2A Squared p66 alpha. [refseq;acc:nm_017660] 81888.8 56306.5 1.45434
POLE4 Rooted dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 44.849 54.7964 1.2218
135 ATG3 Measured apg3p; pc3-96 protein. [refseq;acc:nm_022488] 21785.2 16426.1 1.32626
CPEB4 Ranked cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 350 290 1.2069
GATAD2B Squared transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 81888.8 56306.5 1.45434
NCBP2 Rooted 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 54.935 66.6101 1.21253
136 no value Squared tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 81888.8 56306.5 1.45434
ADIPOR2 Rooted adiponectin receptor 2. [refseq;acc:nm_024551] 41.8357 50.6469 1.21061

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/