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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
green
red
network_comparison
113 Squared myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 12542.6 19321 1.54043
Rooted beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 101.526 80.4705 1.26165
114 Measured huntingtin interacting protein c. [refseq;acc:nm_012272] 5807.72 4300.47 1.35048
Ranked kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 267.246 332.874 1.24557
Squared myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 12542.6 19321 1.54043
Rooted beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 101.526 80.4705 1.26165
115 Measured 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 28492 21185 1.34491
Ranked kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 267.246 332.874 1.24557
Squared dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 12542.6 19321 1.54043
Rooted spermatogenesis associated 6. [refseq;acc:nm_019073] 101.526 80.4705 1.26165
116 Measured pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 28492 21185 1.34491
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 334.483 268.565 1.24545
Squared myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 12542.6 19321 1.54043
Rooted amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 101.526 80.4705 1.26165
117 Measured pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 28492 21185 1.34491
Ranked neuralized-like. [refseq;acc:nm_004210] 266.948 332.326 1.24491
Squared cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 137422 211446 1.53866
Rooted transcription factor jun-b. [swissprot;acc:p17275] 79.5311 63.4173 1.25409
118 Measured pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 28492 21185 1.34491
Ranked 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] 228.934 284.753 1.24382
Squared poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 136779 210445 1.53858
Rooted homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 62.9788 50.3065 1.2519
119 Measured mitochondrial solute carrier protein. [refseq;acc:nm_145305] 28492 21185 1.34491
Ranked 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] 259.004 318.982 1.23157
Squared exocyst complex component sec5. [swissprot;acc:q96kp1] 136716 210335 1.53848
Rooted ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 62.9892 50.3247 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] 6895.98 5136.78 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] 327.709 269.278 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] 136638 210199 1.53836
Rooted homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 62.9942 50.3333 1.25154
121 Measured transcription factor jun-b. [swissprot;acc:p17275] 7488.4 5579.18 1.3422
Ranked cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 327.655 269.254 1.2169
Squared serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 130021 199594 1.53509
Rooted homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 62.9975 50.339 1.25147
122 Measured high-mobility group 20a. [refseq;acc:nm_018200] 6893.53 5140.14 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] 327.642 269.248 1.21688
Squared cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 131906 201896 1.53061
Rooted transcription factor jun-d. [swissprot;acc:p17535] 79.6225 63.636 1.25122
123 Measured cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 18172.1 24260.3 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] 327.601 269.23 1.21681
Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 126167 192904 1.52896
Rooted nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 67.9743 54.6527 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] 18168.9 24255.7 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] 171.595 208.52 1.21519
Squared type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 126095 192779 1.52884
Rooted nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 67.9477 54.6625 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] 18168.9 24255.7 1.33501
Ranked high-mobility group 20a. [refseq;acc:nm_018200] 171.778 208.588 1.21429
Squared ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 124480 189976 1.52616
Rooted small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 67.934 54.8203 1.23921

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/