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 [...,...].
Gene Value Type Rank description Network Comparison Type Filtered Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 51 to 100 of 77072 in total
Value Type  : Measured
Rank
description
Network Comparison Type
Filtered
Interaction Map
red
network_comparison
green
7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Divided 1 Low confidence 736.5 2.86965 2113.5
sedlin. [swissprot;acc:o14582] 0 High confidence 0.00001 4300000 43
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 1 1153.5 3.39764 339.5
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] 0 Low confidence 2.31962 231962 0.00001
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Subtracted 1 36360.3 7008.5 43368.8
zinc finger protein 277. [swissprot;acc:q9nrm2] 0 High confidence 13174.7 2430.4 15605.1
8 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided Low confidence 85 75.4118 6410
db83 protein. [swissprot;acc:p57088] 1 High confidence 1153.5 3.39764 339.5
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Subtracted Low confidence 33111.4 6246.7 39358.1
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 0 High confidence 5106.93 2393.82 7500.75
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1 21185 7307 28492
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Divided Low confidence 3278 1.54317 5058.5
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 0 High confidence 0.00001 4300000 43
zinc finger protein 277. [swissprot;acc:q9nrm2] Subtracted Low confidence 7537.89 1232.83 8770.72
9 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] High confidence 12478 2278 14756
Low confidence 10255.7 1212.6 11468.3
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided High confidence 85 75.4118 6410
n33 protein. [swissprot;acc:q13454] 1 Low confidence 3278 1.54317 5058.5
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Subtracted High confidence 21185 7307 28492
sperm associated antigen 7. [refseq;acc:nm_004890] Low confidence 23318 4037.2 19280.8
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Divided High confidence 398.5 3.21581 1281.5
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 0 Low confidence 383.762 36.1876 10.6048
10 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Subtracted 1593 1211 2804
implantation-associated protein. [refseq;acc:nm_032121] Divided 1 3278 1.54317 5058.5
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 High confidence 85 75.4118 6410
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted 7830.62 1637.55 6193.07
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 1 21185 7307 28492
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Low confidence 19498.1 2232.7 17265.4
serpin b12. [swissprot;acc:q96p63] Divided 0 199.549 35.8425 5.56738
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 1 High confidence 398.5 3.21581 1281.5
11 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 0 5734.28 1517.74 7252.02
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Low confidence 4230.36 1111.45 5341.81
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Divided 1 High confidence 398.5 3.21581 1281.5
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 0 Low confidence 199.249 34.8539 5.71669
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Subtracted 1 High confidence 21185 7307 28492
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence 7256.71 2112.16 9368.87
serpin b12. [swissprot;acc:q96p63] Divided 0 High confidence 199.549 35.8425 5.56738
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 1 Low confidence 1917.64 1.53861 2950.5
12 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 0 High confidence 5629.62 1469.89 7099.51
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided 1 398.5 3.21581 1281.5
gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 1921.96 1.5371 2954.24
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 15464.1 2108.6 17572.7
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Divided 0 High confidence 199.249 34.8539 5.71669
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 859 14.8103 58
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 1 High confidence 34190.9 6604.9 40795.8
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 0 Low confidence 31122 1099.6 30022.4
13 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided High confidence 1363 29 47
Subtracted 1316
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Divided 1 398.5 3.21581 1281.5
fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] 0 Low confidence 8.11997 14.21 115.385

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/