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 4608 to 4657 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
576 limkain b1. [refseq;acc:nm_019081] Squared Subtracted 31994 36719.6 4725.6
577 60s ribosomal protein l15. [swissprot;acc:p39030] Ranked 217.862 230.978 13.116
acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] Squared Divided 36109.8 42811.6 1.1856
band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Measured Subtracted 7813.45 8570.07 756.62
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Ranked Divided 224.606 210.944 1.06477
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Measured 6739.81 7644.62 1.13425
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Rooted 121.695 131.815 1.08316
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Subtracted 50.3803 45.4193 4.961
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Squared 31994 36719.6 4725.6
578 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Rooted 50.3803 45.4193 4.961
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Measured Divided 6739.81 7644.62 1.13425
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Rooted 121.695 131.815 1.08316
importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Squared 23534.9 27890.2 1.18506
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] Ranked Subtracted 15 28 13
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Measured 7813.35 8569.96 756.61
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Ranked Divided 224.606 210.944 1.06477
579 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] Measured Subtracted 7813.34 8569.95 756.61
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Ranked 15 28 13
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Squared 31994 36719.6 4725.6
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Measured Divided 6739.82 7644.62 1.13425
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Rooted 121.695 131.815 1.08316
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Subtracted 63.1463 68.1044 4.9581
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Squared Divided 23526.4 27879.4 1.18503
zinc finger protein t86. [swissprot;acc:o00488] Ranked 246.805 231.796 1.06475
580 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Measured Subtracted 7813.36 8569.97 756.61
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Ranked 15 28 13
dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] Rooted 63.1463 68.1044 4.9581
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Measured Divided 6739.83 7644.63 1.13425
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Rooted 121.695 131.815 1.08316
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Squared Subtracted 31994 36719.6 4725.6
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Divided 23526.4 27879.3 1.18502
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Ranked 236.751 252.038 1.06457
581 cytohesin 4. [swissprot;acc:q9uia0] Subtracted 15 28 13
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Squared 31994 36719.6 4725.6
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Measured 7810.11 8566.29 756.18
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Divided 6739.82 7644.63 1.13425
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Rooted 121.695 131.815 1.08316
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Subtracted 59.7294 64.6872 4.9578
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Ranked Divided 237.28 252.492 1.06411
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Squared 23526.4 27879.3 1.18502
582 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Ranked Subtracted 15 28 13
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Squared 31994 36719.6 4725.6
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Measured Divided 6739.82 7644.62 1.13425
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] Ranked 237.28 252.492 1.06411
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Rooted 121.695 131.815 1.08316
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Subtracted 59.7294 64.6872 4.9578
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Measured 6834.54 7590.49 755.95
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Squared Divided 23526.4 27879.3 1.18502
583 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]

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/