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 168 to 217 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
84 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 0 973.698 1601.52 1.64478
85 fos-related antigen 2. [swissprot;acc:p15408] 1 4941.95 7037.11 1.42395
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] 0 679.449 1106.88 1.62908
86 alpha crystallin a chain. [swissprot;acc:p02489] 55.3059 89.2447 1.61366
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 1 4942.49 7037.32 1.42384
87 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 4944.3 7038.04 1.42347
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] 0 304.664 483.809 1.58801
88 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 1 2411.93 1695.45 1.42259
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] 0 304.664 483.809 1.58801
89 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 1 2414.22 1698.12 1.4217
suppressor of actin 1. [refseq;acc:nm_014016] 0 23.6076 37.4843 1.58781
90 metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] 34.6667 54.6667 1.57692
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] 1 2414.77 1698.75 1.4215
91 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 2416.53 1700.8 1.42082
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 0 39.7924 62.2106 1.56338
92 adp-ribosylation factor 3. [swissprot;acc:p16587] 300.697 469.346 1.56086
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 1 4117.67 5801.04 1.40882
93 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 0 528.5 816.5 1.54494
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 1 4245.52 5942.75 1.39977
94 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 4247.86 5941.88 1.39879
myosin vi. [swissprot;acc:q9um54] 0 345.865 224.096 1.54338
95 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 154 0.00001 15400000
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] 1 2397.19 3343.62 1.39481
96 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 4110.14 5694.99 1.3856
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0 154 0.00001 15400000
97 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 728.65 476.619 1.52879
amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 1 2820.51 3897.1 1.3817
98 pp3111 protein. [refseq;acc:nm_022156] 0 789 530 1.48868
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 1 2353.63 3225.65 1.3705
99 s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] 0 817.81 551.434 1.48306
100 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] 594 402 1.47761
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 1 2353.63 3225.65 1.3705
101 cullin homolog 2 (cul-2). [swissprot;acc:q13617]
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 0 1442 977 1.47595
102 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 1 2353.63 3225.65 1.3705
103 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 0 197.333 290.667 1.47298
104 musashi 2 isoform a. [refseq;acc:nm_138962] 1 4241.57 5810.79 1.36996
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 0 5106.93 7500.75 1.46874
105 fos-related antigen 2. [swissprot;acc:p15408] 3233.86 2208.1 1.46454
musashi 1. [refseq;acc:nm_002442] 1 4241.57 5810.79 1.36996
106 nuclear protein ukp68. [refseq;acc:nm_024824]
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 0 1251.66 858.525 1.45792
107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 1 4266.04 5843.51 1.36977
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 0 326.677 472.605 1.4467
108 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 292 421 1.44178
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 1 4366.44 5899.76 1.35116
109 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 0 100 144 1.44

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/