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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 773 to 822 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
network_comparison
red
green
387 Divided no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 1.09029 242.238 264.11
Subtracted ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 18.6763 56.6768 75.3531
388 Divided no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 1.09015 227.575 208.756
Subtracted MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 18.6704 56.7244 75.3948
389 Divided SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 1.09015 227.575 208.756
Subtracted MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 18.6702 56.7252 75.3954
390 Divided MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 1.09011 241.828 263.62
Subtracted ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 18.6629 56.7841 75.447
391 Divided RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] 1.09011 241.828 263.62
Subtracted TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 18.647 225.719 207.072
392 Divided RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 1.09008 241.83 263.615
Subtracted POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 18.613 239.092 257.705
393 Divided TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 1.09005 225.719 207.072
Subtracted POLR3F dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 18.406 238.921 257.327
394 Divided DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 1.08948 218.827 238.407
Subtracted CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 18.337 207.889 226.226
395 Divided DPP8 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 1.08948 218.827 238.407
Subtracted PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] 18.31 207.908 226.218
396 Divided no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 1.08945 240.801 262.34
Subtracted RPA1 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] 18.31 207.908 226.218
397 Divided CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 1.08932 110.689 101.613
Subtracted RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] 18.31 207.908 226.218
398 Divided ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 1.0893 218.818 238.358
Subtracted PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 18.31 207.908 226.218
399 Divided CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 1.08821 207.889 226.226
Subtracted RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] 18.31 207.908 226.218
400 Divided PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] 1.08807
Subtracted CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 18.278 207.931 226.209
401 Divided RPA1 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] 1.08807 207.908 226.218
Subtracted MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 18.21 254.434 236.224
402 Divided RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] 1.08807 207.908 226.218
Subtracted NDC80 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 18.181 231.802 249.983
403 Divided PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 1.08807 207.908 226.218
Subtracted MACF1 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] 17.87 228.468 246.338
404 Divided RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] 1.08807 207.908 226.218
Subtracted DST bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 17.867 228.463 246.33
405 Divided CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 1.0879 207.931 226.209
Subtracted GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 17.5875 65.4586 83.0461
406 Divided no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 1.08731 265.634 244.304
Subtracted NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 17.558 237.109 254.667
407 Divided MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 1.08673 239.75 260.544
Subtracted NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 17.558 237.109 254.667
408 Divided CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 1.08649 255.112 234.804
Subtracted HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 17.558 237.109 254.667
409 Divided POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] 1.08641 241.045 261.874
Subtracted RUNX2 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] 17.558 237.109 254.667
410 Divided no value tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 1.0864 233.376 253.539
Subtracted HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 17.558 237.109 254.667
411 Divided GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] 1.0864 233.376 253.539
Subtracted RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] 17.558 237.109 254.667

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/