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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1508 to 1557 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
Interaction Map
red
green
network_comparison
377 POLR1A Divided dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] High confidence 242.691 265.481 1.09391
378 FEM1B Subtracted fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 248.152 267.226 19.074
LDHC Divided l-lactate dehydrogenase c chain (ec 1.1.1.27) (ldh-c) (ldh testis subunit) (ldh-x). [swissprot;acc:p07864] Low confidence 205.928 198.554 1.03714
RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] High confidence 242.593 265.365 1.09387
SLC35E1 Subtracted solute carrier family 35, member e1. [refseq;acc:nm_024881] Low confidence 203.661 211.03 7.369
379 AK2 Divided adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] High confidence 241.509 264.163 1.0938
LDHA l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] Low confidence 205.928 198.554 1.03714
LRRC3 Subtracted leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] High confidence 248.152 267.226 19.074
MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Low confidence 205.921 198.554 7.367
380 no value Divided suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] High confidence 242.109 264.79 1.09368
LAMC1 Subtracted laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 248.152 267.226 19.074
LDHB Divided l-lactate dehydrogenase b chain (ec 1.1.1.27) (ldh-b) (ldh heart subunit) (ldh-h). [swissprot;acc:p07195] Low confidence 205.928 198.554 1.03714
RAB24 Subtracted max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 205.918 7.364
381 CLASP1 Divided clip-associating protein 1; drosophila 'multiple asters' (mast)-like homolog 1. [refseq;acc:nm_015282] 205.928 1.03714
POLE4 Subtracted dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 205.821 198.494 7.327
SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] High confidence 248.152 267.226 19.074
TAF7 Divided transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 200.586 183.423 1.09357
382 no value Subtracted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 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 Divided max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 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 Subtracted homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 162.755 155.476 7.279
MXD4 Divided max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 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 Subtracted trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 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 Divided 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] 266.421 244.236 1.09083
HOXC5 Subtracted homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence 162.755 155.476 7.279
RAB24 Divided max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 205.918 198.554 1.03709
385 no value Subtracted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 162.755 155.476 7.279
E2F2 Divided transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 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 Subtracted small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 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 Divided dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 205.821 198.494 1.03691
RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] High confidence 242.238 264.11 1.09029
RPS9 Subtracted 40s ribosomal protein s9. [swissprot;acc:p46781] 238.986 257.784 18.798
387 no value Divided 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 242.238 264.11 1.09029
ATG4A Subtracted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 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 Divided serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 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 Subtracted homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 162.755 155.476 7.279
HTRA3 Divided probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 200.049 192.942 1.03683
MAP1LC3B Subtracted microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 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 Divided probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 200.049 192.942 1.03683
MAP1LC3A Subtracted microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] High confidence 56.7252 75.3954 18.6702
SNRPF Divided small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 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

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/