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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 113 to 162 of 502 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 0
Rank
Hugo
description
red
green
network_comparison
113 DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 5673.33 6797.56 1.19816
114 no value bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 8871.11 10603.2 1.19525
115 spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 18662.8 15627 1.19427
116 MTX1 metaxin 1. [swissprot;acc:q13505] 13761.3 16422.1 1.19335
117 no value basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 11545 13771.5 1.19285
118 AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 12049 14370.7 1.19269
119 no value mesoderm induction early response 1. [refseq;acc:nm_020948] 3609 4302.5 1.19216
120 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 5797 4873 1.18962
121 ZNF232 zinc finger protein 232. [swissprot;acc:q9uny5] 11523.7 13686.9 1.18772
122 ZNF24 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 11523 13685.4 1.18766
123 ZNF215 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 11522.8 13684.9 1.18764
124 no value zinc finger imprinted 2. [swissprot;acc:q9nzv7] 11520.7 13680.4 1.18746
125 PIK3C2B phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 22038 18578 1.18624
126 no value ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 9722.71 11493.8 1.18216
127 PDSS1 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 9411.34 11119.7 1.18152
128 no value 60s ribosomal protein l39. [swissprot;acc:p02404] 11564.4 9794.29 1.18073
129 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 14222.5 12058.6 1.17945
130 enigma protein; lim domain protein. [refseq;acc:nm_005451] 14476.2 17069.5 1.17914
131 MLH1 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 8375.43 9873.58 1.17887
132 no value rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 19048 22389 1.1754
133 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 6814 8009 1.17537
134 CYP4F8 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 12314.9 10489.3 1.17404
135 CYP4F2 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]
136 CYP4F12 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 12335.3 10506.8 1.17403
137 CYP4F11 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 12328.5 10501
138 CYP4X1 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 12384.7 10549.4 1.17397
139 CRYAA alpha crystallin a chain. [swissprot;acc:p02489] 16372.4 13972.2 1.17178
140 no value mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 16411.9 14027.1 1.17001
141 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 7690.02 8991.19 1.1692
142 CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 8214.41 7026.41 1.16908
143 no value dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] 11124.8 13005.3 1.16904
144 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 11123.4 13000.1 1.16872
145 SRI sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 7955.61 6817.49 1.16694
146 COPB2 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 12577.8 14662.1 1.16571
147 no value 60s ribosomal protein l7. [swissprot;acc:p18124] 11080.3 9505.89 1.16562
148 SPTBN5 spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 6755.71 7863.63 1.164
149 no value block 23. [sptrembl;acc:q8nhw5] 11469.3 13334.8 1.16265
150 ZFPL1 zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] 8730 7516 1.16152
151 no value u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 7502.08 6461.83 1.16098
152 similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 11438 13277.1 1.16079
153 TUBG1 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] 7879.3 6789.92 1.16044
154 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 10883 12622.8 1.15986
155 REEP6 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 12759.4 11028.8 1.15692
156 TUB tubby protein homolog. [swissprot;acc:p50607] 12303.7 10641.7 1.15618
157 no value transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 18079 15652 1.15506
158 NME2P1 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 10060.2 11616.4 1.15469
159 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 5813.32 6706.32 1.15361
160 no value ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 11732 13530.6 1.15331
161 ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 5781.93 6660.63 1.15197
162 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 12301.4 10680.5 1.15176

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
- Hugo is the HGNC identifier if it exists
- 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/