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 description Value Type Network Comparison Type Interaction Map Filtered network_comparison red 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
network_comparison
red
green
113 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked 1.24557 332.874 267.246
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared 1.54043 19321 12542.6
114 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Rooted 1.26165 80.4705 101.526
huntingtin interacting protein c. [refseq;acc:nm_012272] Measured 1.35048 4300.47 5807.72
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked 1.24557 332.874 267.246
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Squared 1.54043 19321 12542.6
115 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Measured 1.34491 21185 28492
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Squared 1.54043 19321 12542.6
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Ranked 1.24557 332.874 267.246
spermatogenesis associated 6. [refseq;acc:nm_019073] Rooted 1.26165 80.4705 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 1.24545 268.565 334.483
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared 1.54043 19321 12542.6
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Measured 1.34491 21185 28492
117 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared 1.53866 211446 137422
neuralized-like. [refseq;acc:nm_004210] Ranked 1.24491 332.326 266.948
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Measured 1.34491 21185 28492
transcription factor jun-b. [swissprot;acc:p17275] Rooted 1.25409 63.4173 79.5311
118 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 1.2519 50.3065 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 1.24382 284.753 228.934
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Measured 1.34491 21185 28492
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Squared 1.53858 210445 136779
119 exocyst complex component sec5. [swissprot;acc:q96kp1] 1.53848 210335 136716
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Measured 1.34491 21185 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 1.23157 318.982 259.004
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Rooted 1.25166 50.3247 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 1.34247 5136.78 6895.98
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Rooted 1.25154 50.3333 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 1.53836 210199 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 1.21699 269.278 327.709
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 1.2169 269.254 327.655
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Rooted 1.25147 50.339 62.9975
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 1.53509 199594 130021
transcription factor jun-b. [swissprot;acc:p17275] Measured 1.3422 5579.18 7488.4
122 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared 1.53061 201896 131906
high-mobility group 20a. [refseq;acc:nm_018200] Measured 1.34112 5140.14 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 1.21688 269.248 327.642
transcription factor jun-d. [swissprot;acc:p17535] Rooted 1.25122 63.636 79.6225
123 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured 1.33503 24260.3 18172.1
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 1.24375 54.6527 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 1.21681 269.23 327.601
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 1.52896 192904 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 1.21519 208.52 171.595
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 1.33501 24255.7 18168.9
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 1.24304 54.6625 67.9477
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared 1.52884 192779 126095
125 high-mobility group 20a. [refseq;acc:nm_018200] Ranked 1.21429 208.588 171.778
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured 1.33501 24255.7 18168.9
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 1.52616 189976 124480
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted 1.23921 54.8203 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/