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 network_comparison green
Results: HTML CSV LaTeX Showing element 451 to 500 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
network_comparison
green
113 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked 332.874 1.24557 267.246
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared 19321 1.54043 12542.6
114 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Rooted 80.4705 1.26165 101.526
huntingtin interacting protein c. [refseq;acc:nm_012272] Measured 4300.47 1.35048 5807.72
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked 332.874 1.24557 267.246
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Squared 19321 1.54043 12542.6
115 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Measured 21185 1.34491 28492
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Squared 19321 1.54043 12542.6
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Ranked 332.874 1.24557 267.246
spermatogenesis associated 6. [refseq;acc:nm_019073] Rooted 80.4705 1.26165 101.526
116 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Ranked 268.565 1.24545 334.483
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared 19321 1.54043 12542.6
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Measured 21185 1.34491 28492
117 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared 211446 1.53866 137422
neuralized-like. [refseq;acc:nm_004210] Ranked 332.326 1.24491 266.948
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Measured 21185 1.34491 28492
transcription factor jun-b. [swissprot;acc:p17275] Rooted 63.4173 1.25409 79.5311
118 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 50.3065 1.2519 62.9788
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Ranked 284.753 1.24382 228.934
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Measured 21185 1.34491 28492
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Squared 210445 1.53858 136779
119 exocyst complex component sec5. [swissprot;acc:q96kp1] 210335 1.53848 136716
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Measured 21185 1.34491 28492
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 1.23157 259.004
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Rooted 50.3247 1.25166 62.9892
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 1.34247 6895.98
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Rooted 50.3333 1.25154 62.9942
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Squared 210199 1.53836 136638
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 1.21699 327.709
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 1.2169 327.655
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Rooted 50.339 1.25147 62.9975
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 199594 1.53509 130021
transcription factor jun-b. [swissprot;acc:p17275] Measured 5579.18 1.3422 7488.4
122 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared 201896 1.53061 131906
high-mobility group 20a. [refseq;acc:nm_018200] Measured 5140.14 1.34112 6893.53
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 1.21688 327.642
transcription factor jun-d. [swissprot;acc:p17535] Rooted 63.636 1.25122 79.6225
123 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured 24260.3 1.33503 18172.1
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 1.24375 67.9743
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 1.21681 327.601
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 192904 1.52896 126167
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 1.21519 171.595
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 24255.7 1.33501 18168.9
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 54.6625 1.24304 67.9477
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared 192779 1.52884 126095
125 high-mobility group 20a. [refseq;acc:nm_018200] Ranked 208.588 1.21429 171.778
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured 24255.7 1.33501 18168.9
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 189976 1.52616 124480
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted 54.8203 1.23921 67.934

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/