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 Value Type description 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
Value Type
description
red
green
network_comparison
119 Squared exocyst complex component sec5. [swissprot;acc:q96kp1] 210335 136716 1.53848
Rooted ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 50.3247 62.9892 1.25166
120 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
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
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
Rooted homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 50.3333 62.9942 1.25154
121 Measured transcription factor jun-b. [swissprot;acc:p17275] 5579.18 7488.4 1.3422
Ranked cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 327.655 1.2169
Squared serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 199594 130021 1.53509
Rooted homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 50.339 62.9975 1.25147
122 Measured high-mobility group 20a. [refseq;acc:nm_018200] 5140.14 6893.53 1.34112
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
Squared cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 201896 131906 1.53061
Rooted transcription factor jun-d. [swissprot;acc:p17535] 63.636 79.6225 1.25122
123 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
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
Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 192904 126167 1.52896
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 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
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
Squared type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 192779 126095 1.52884
Rooted nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 54.6625 67.9477 1.24304
125 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
Ranked high-mobility group 20a. [refseq;acc:nm_018200] 208.588 171.778 1.21429
Squared ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 189976 124480 1.52616
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 Measured cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 24250 18164.9 1.33499
Ranked associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 94 114 1.21277
Squared serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 189976 124480 1.52616
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
127 Measured transcription factor jun-d. [swissprot;acc:p17535] 5638.2 7523.39 1.33436
Ranked putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 94 114 1.21277
Squared cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 88432.6 58423.3 1.51365
Rooted high-mobility group 20a. [refseq;acc:nm_018200] 60.9353 75.094 1.23236
128 Measured luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 4355.61 5810.82 1.3341
Ranked associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 94 114 1.21277
Squared pnas-18. [sptrembl;acc:q9bzu3] 87787.3 58155.8 1.50952
Rooted tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 48.0515 39.0445 1.23069
129 Measured luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 4358.13 5811.49 1.33348
Ranked neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 94 114 1.21277
Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 178263 118639 1.50257
Rooted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 54.2343 66.7323 1.23044
130 Measured forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 2234.68 2978.53 1.33287
Ranked protein hspc134 (protein cda04). [swissprot;acc:q9by43] 94 114 1.21277
Squared 44050 protein. [refseq;acc:nm_178832] 148058 99628.4 1.4861
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
131 Measured forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 2234.73 2978.57 1.33285
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
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
Rooted huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 55.1113 67.5537 1.22577

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/