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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3101 to 3150 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
388 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Subtracted High confidence 1 56.7244 75.3948 18.6704
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Divided 0 9953.39 10320.9 1.03692
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Low confidence 1 200.049 192.942 1.03683
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] High confidence 227.575 208.756 1.09015
389 abl-philin 2. [refseq;acc:nm_032327] Low confidence 0 16315 17688 1.08416
calcyphosine. [swissprot;acc:q13938] Subtracted 10007.1 9350.72 656.38
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 1 162.755 155.476 7.279
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Divided High confidence 0 11794.7 11375.4 1.03686
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 1 56.7252 75.3954 18.6702
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Divided Low confidence 200.049 192.942 1.03683
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] High confidence 227.575 208.756 1.09015
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Subtracted 0 10481.8 10869.5 387.7
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Divided 1 241.828 263.62 1.09011
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Subtracted 0 10449 10061.8 387.2
alpha-nac protein. [sptrembl;acc:q9h009] Divided 14204.4 14724.5 1.03662
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Low confidence 11847.5 12843.9 1.0841
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted High confidence 1 56.7841 75.447 18.6629
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence 162.755 155.476 7.279
solute carrier family 35, member e2. [refseq;acc:nm_182838] Divided 203.647 211.144 1.03681
synaptotagmin xiv. [refseq;acc:nm_153262] Subtracted 0 9414 10068.8 654.8
391 40s ribosomal protein s16. [swissprot;acc:p17008] Divided High confidence 1 241.828 263.62 1.09011
alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Subtracted Low confidence 0 11645.4 12290.5 645.1
dead-box protein. [refseq;acc:nm_018665] Divided 9591.43 10391.6 1.08343
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] High confidence 14223.9 14738.5 1.03618
rna binding protein. [refseq;acc:nm_032509] Subtracted Low confidence 1 206.88 199.607 7.273
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Divided 200.046 192.943 1.03681
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted High confidence 225.719 207.072 18.647
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 0 10302.7 10686.7 384
392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Divided 1 241.83 263.615 1.09008
alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] Low confidence 0 9851.59 10670.2 1.08309
leptin receptor gene-related protein (ob-r gene related protein) (ob- rgrp). [swissprot;acc:o15243] Subtracted 1 206.88 199.607 7.273
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Divided 200.894 193.766 1.03679
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Subtracted High confidence 239.092 257.705 18.613
seven in absentia homolog 1. [refseq;acc:nm_003031] Divided 0 9854.67 10201.4 1.03518
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Subtracted 10303.7 10687.4 383.7
tubulointerstitial nephritis antigen. [refseq;acc:nm_014464] Low confidence 15810 15165 645
393 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 11842.3 12486.3 644
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] High confidence 1 238.921 257.327 18.406
leptin receptor overlapping transcript-like 1 (my047 protein). [swissprot;acc:o95214] Low confidence 206.88 199.607 7.273
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Divided 0 9339.12 10115 1.08308
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 1 201.334 194.242 1.03651
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] High confidence 225.719 207.072 1.09005
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 0 12576 13010 1.03451
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Subtracted 5540 5921 381
394 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 10196.9 9857.79 1.0344
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Subtracted 1 207.889 226.226 18.337
cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 0 11816 11175.5 640.5
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided 1 204.815 197.606 1.03648
Subtracted 7.209
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Divided High confidence 218.827 238.407 1.08948

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/