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.


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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 477 to 526 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
120 HMG20B Measured 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] 5136.78 6895.98 1.34247
HOMER1 Rooted homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 50.3333 62.9942 1.25154
KCND2 Ranked potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 269.278 327.709 1.21699
PAPOLG Squared poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 210199 136638 1.53836
121 CTH Ranked cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 327.655 1.2169
HOMER3 Rooted homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 50.339 62.9975 1.25147
JUNB Measured transcription factor jun-b. [swissprot;acc:p17275] 5579.18 7488.4 1.3422
PPP1CC Squared serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 199594 130021 1.53509
122 CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 201896 131906 1.53061
HMG20A Measured high-mobility group 20a. [refseq;acc:nm_018200] 5140.14 6893.53 1.34112
JUND Rooted transcription factor jun-d. [swissprot;acc:p17535] 63.636 79.6225 1.25122
KCND3 Ranked potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] 269.248 327.642 1.21688
123 ATG4A Measured cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 24260.3 18172.1 1.33503
KCND1 Ranked potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 269.23 327.601 1.21681
PPP1R2 Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 192904 126167 1.52896
TIA1 Rooted nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 54.6527 67.9743 1.24375
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

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/