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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 475 to 524 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
119 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Ranked 318.982 259.004 1.23157
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Rooted 50.3247 62.9892 1.25166
120 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] Measured 5136.78 6895.98 1.34247
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Rooted 50.3333 62.9942 1.25154
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Squared 210199 136638 1.53836
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked 269.278 327.709 1.21699
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 327.655 1.2169
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Rooted 50.339 62.9975 1.25147
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 199594 130021 1.53509
transcription factor jun-b. [swissprot;acc:p17275] Measured 5579.18 7488.4 1.3422
122 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared 201896 131906 1.53061
high-mobility group 20a. [refseq;acc:nm_018200] Measured 5140.14 6893.53 1.34112
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] Ranked 269.248 327.642 1.21688
transcription factor jun-d. [swissprot;acc:p17535] Rooted 63.636 79.6225 1.25122
123 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured 24260.3 18172.1 1.33503
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 67.9743 1.24375
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Ranked 269.23 327.601 1.21681
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 192904 126167 1.52896
124 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] Ranked 208.52 171.595 1.21519
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 24255.7 18168.9 1.33501
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 54.6625 67.9477 1.24304
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared 192779 126095 1.52884
125 high-mobility group 20a. [refseq;acc:nm_018200] Ranked 208.588 171.778 1.21429
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured 24255.7 18168.9 1.33501
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 189976 124480 1.52616
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted 54.8203 67.934 1.23921
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked 94 114 1.21277
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured 24250 18164.9 1.33499
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] Rooted 60.9342 75.1387 1.23311
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Squared 189976 124480 1.52616
127 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 88432.6 58423.3 1.51365
high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 75.094 1.23236
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Ranked 94 114 1.21277
transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 7523.39 1.33436
128 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Ranked 94 114 1.21277
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured 4355.61 5810.82 1.3341
pnas-18. [sptrembl;acc:q9bzu3] Squared 87787.3 58155.8 1.50952
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 39.0445 1.23069
129 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 54.2343 66.7323 1.23044
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured 4358.13 5811.49 1.33348
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Ranked 94 114 1.21277
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 178263 118639 1.50257
130 44050 protein. [refseq;acc:nm_178832] 148058 99628.4 1.4861
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Measured 2234.68 2978.53 1.33287
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Rooted 55.1026 67.5701 1.22626
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked 94 114 1.21277
131 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Measured 2234.73 2978.57 1.33285
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Rooted 55.1113 67.5537 1.22577
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] Squared 148058 99628.4 1.4861
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] Ranked 294.053 242.562 1.21228

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/