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 [...,...].
Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1525 to 1574 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
382 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted Low confidence 162.755 155.476 7.279
DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] High confidence 253.852 234.808 19.044
MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Divided Low confidence 205.926 198.554 1.03713
TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] High confidence 200.791 183.66 1.09328
383 HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Subtracted Low confidence 162.755 155.476 7.279
MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Divided 205.921 198.554 1.0371
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] High confidence 237.862 217.739 1.09242
TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Subtracted 236.245 255.113 18.868
384 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 227.575 208.756 18.819
E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Divided 266.421 244.236 1.09083
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted Low confidence 162.755 155.476 7.279
RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided 205.918 198.554 1.03709
385 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 162.755 155.476 7.279
E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided High confidence 266.421 244.236 1.09083
SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Low confidence 201.176 193.984 1.03708
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Subtracted High confidence 227.575 208.756 18.819
386 HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 162.755 155.476 7.279
POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Divided 205.821 198.494 1.03691
RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] High confidence 242.238 264.11 1.09029
RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] Subtracted 238.986 257.784 18.798
387 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Divided 242.238 264.11 1.09029
ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 56.6768 75.3531 18.6763
HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Low confidence 162.755 155.476 7.279
HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Divided 200.057 192.938 1.0369
388 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] High confidence 227.575 208.756 1.09015
HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted Low confidence 162.755 155.476 7.279
HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Divided 200.049 192.942 1.03683
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Subtracted High confidence 56.7244 75.3948 18.6704
389 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 162.755 155.476 7.279
HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Divided 200.049 192.942 1.03683
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted High confidence 56.7252 75.3954 18.6702
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Divided 227.575 208.756 1.09015
390 no value solute carrier family 35, member e2. [refseq;acc:nm_182838] Low confidence 203.647 211.144 1.03681
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted High confidence 56.7841 75.447 18.6629
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence 162.755 155.476 7.279
MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Divided High confidence 241.828 263.62 1.09011
391 no value rna binding protein. [refseq;acc:nm_032509] Subtracted Low confidence 206.88 199.607 7.273
HTRA2 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
RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] High confidence 241.828 263.62 1.09011
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted 225.719 207.072 18.647
392 LEPR leptin receptor gene-related protein (ob-r gene related protein) (ob- rgrp). [swissprot;acc:o15243] Low confidence 206.88 199.607 7.273
NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Divided 200.894 193.766 1.03679
POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Subtracted High confidence 239.092 257.705 18.613
RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Divided 241.83 263.615 1.09008
393 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Low confidence 201.334 194.242 1.03651
LEPROTL1 leptin receptor overlapping transcript-like 1 (my047 protein). [swissprot;acc:o95214] Subtracted 206.88 199.607 7.273
POLR3F dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] High confidence 238.921 257.327 18.406
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Divided 225.719 207.072 1.09005
394 CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Subtracted 207.889 226.226 18.337
CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided Low confidence 204.815 197.606 1.03648

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/