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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Hugo measured Gene Rank expected description final
Results: HTML CSV LaTeX Showing element 2858 to 2907 of 3206 in total
Hugo
measured
Rank
expected
description
final
SUV39H1 0.027437 2006 0.118935 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 1 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 1) (H3-K9-HMTASE 1) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1) (SU(VAR)3-9 HOMOLOG 1). [SWISSPROT;Acc:O43463]" 0.230689032
SUV39H2 0.0323264 2008 0.14013 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 2 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 2) (H3-K9-HMTASE 2) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2) (SU(VAR)3-9 HOMOLOG 2). [SWISSPROT;Acc:Q9H5I1]" 0.230688646
SYMPK 0.0685085 2095 0.299686 SYMPLEKIN. [SWISSPROT;Acc:Q92797] 0.228600936
SYN1 0.132875 66 0.327175 SYNAPSIN I (BRAIN PROTEIN 4.1). [SWISSPROT;Acc:P17600] 0.406128219
SYN2 0.159227 69 0.392062 SYNAPSIN II. [SWISSPROT;Acc:Q92777] 0.406127092
SYN3 0.133193 79 0.32796 SYNAPSIN III. [SWISSPROT;Acc:O14994] 0.406125747
SYNCRIP 0.0658169 260 0.213303 NS1-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_006372] 0.308560592
SYT12 0.236204 2782 1.17564 SYNAPTOTAGMIN XII (SYTXII). [SWISSPROT;Acc:Q8IV01] 0.200915246
SYVN1 0.191556 701 0.722002 HRD1 PROTEIN ISOFORM A; SYNOVIOLIN1. [RefSeq;Acc:NM_032431] 0.265312284
T 0.0274799 2453 0.126718 BRACHYURY PROTEIN (T PROTEIN). [SWISSPROT;Acc:O15178] 0.216858694
TADA2L 0.42132 2464 1.94413 TRANSCRIPTIONAL ADAPTER 2-LIKE (ADA2-LIKE PROTEIN) (KL04P). [SWISSPROT;Acc:O75478] 0.216713903
TADA3L 0.0337015 2463 0.155511 TRANSCRIPTIONAL ADAPTOR 3-LIKE ISOFORM A. [RefSeq;Acc:NM_006354] 0.216714573
TAF11 0.343318 1013 1.35164 TRANSCRIPTION INITIATION FACTOR TFIID 28 KDA SUBUNIT (TAFII-28) (TAFII28) (TFIID SUBUNIT P30-BETA). [SWISSPROT;Acc:Q15544] 0.254001065
TAF12 0.396471 2299 1.78321 TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS (TAFII- 20/TAFII-15) (TAFII20/TAFII15). [SWISSPROT;Acc:Q16514] 0.222335563
TAF5 0.331362 2368 1.50518 TRANSCRIPTION INITIATION FACTOR TFIID 100 KDA SUBUNIT (TAFII-100) (TAFII100). [SWISSPROT;Acc:Q15542] 0.220147756
TAF6 0.391086 2348 1.77434 TRANSCRIPTION INITIATION FACTOR TFIID 70 KDA SUBUNIT (TAFII-70) (TAFII-80) (TAFII80). [SWISSPROT;Acc:P49848] 0.220412097
TAF7 0.124527 353 0.441415 TRANSCRIPTION INITIATION FACTOR TFIID 55 KDA SUBUNIT (TAFII-55) (TAFII55). [SWISSPROT;Acc:Q15545] 0.282108673
TAF7L 0.103996 354 0.36903 "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]" 0.281809067
TAF9 0.61918 2669 2.95928 TRANSCRIPTION INITIATION FACTOR TFIID 31 KDA SUBUNIT (TAFII-31) (TAFII-32) (TAFII32). [SWISSPROT;Acc:Q16594] 0.209233327
TAF9B 0.383112 2675 1.83532 "TBP-ASSOCIATED FACTOR 9L; NEURONAL CELL DEATH-RELATED PROTEIN; TAF9-LIKE RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 31 KD; NEURONAL CELL DEATH-RELATED GENE IN NEURON-7; TRANSCRIPTION ASSOCIATED FACTOR TAFII31L; TRANSCRIPTION INIT" 0.208743979
TALDO1 0.0846644 2137 0.371472 TRANSALDOLASE (EC 2.2.1.2). [SWISSPROT;Acc:P37837] 0.227915967
TANC1 0.0385127 823 0.147402 0.261276645
TARDBP 0.653337 1140 2.60974 TAR DNA-BINDING PROTEIN-43 (TDP-43). [SWISSPROT;Acc:Q13148] 0.250345628
TARSL2 0.179735 2780 0.894194 0.201002243
TATDN1 0.378654 1777 1.60733 CDA11 PROTEIN. [RefSeq;Acc:NM_032026] 0.235579501
TBC1D10A 0.2166 1027 0.854644 EBP50-PDZ INTERACTOR OF 64 KDA (EPI64 PROTEIN). [SWISSPROT;Acc:Q9BXI6] 0.253438859
TBC1D10B 0.178897 1022 0.705791 0.25347022
TBC1D22A 0.046789 551 0.172653 TBC1 DOMAIN FAMILY PROTEIN C22ORF4. [SWISSPROT;Acc:Q8WUA7] 0.271000214
TBC1D22B 0.0359807 559 0.132771 TBC1 DOMAIN FAMILY PROTEIN C22ORF4-LIKE (FRAGMENT). [SWISSPROT;Acc:Q9NU19] 0.270998185
TBC1D5 0.115058 2643 0.547991 TBC1 DOMAIN FAMILY MEMBER 5. [SWISSPROT;Acc:Q92609] 0.209963302
TBCC 0.0292681 2971 0.208597 TUBULIN-SPECIFIC CHAPERONE C (TUBULIN-FOLDING COFACTOR C) (CFC). [SWISSPROT;Acc:Q15814] 0.140309305
TBL1X 0.0306345 1420 0.125605 "TRANSDUCIN BETA-LIKE 1X PROTEIN (TRANSDUCIN-BETA-LIKE 1, X-LINKED). [SWISSPROT;Acc:O60907]" 0.243895546
TBL1Y 0.0303893 1421 0.1246 "TRANSDUCIN BETA-LIKE 1Y PROTEIN (TRANSDUCIN-BETA-LIKE 1, Y-LINKED). [SWISSPROT;Acc:Q9BQ87]" 0.243894864
TBL2 0.132041 454 0.478695 TRANSDUCIN BETA-LIKE 2 PROTEIN (WS BETA-TRANSDUCIN REPEATS PROTEIN) (WS-BETATRP) (WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 13 PROTEIN). [SWISSPROT;Acc:Q9Y4P3] 0.275835344
TBL3 0.306804 1442 1.26013 TRANSDUCIN BETA-LIKE 3; WD-REPEAT PROTEIN SAZD. [RefSeq;Acc:NM_006453] 0.243470118
TBP 0.0386201 1191 0.155349 TATA BOX BINDING PROTEIN (TRANSCRIPTION INITIATION FACTOR TFIID) (TATA-BOX FACTOR) (TATA SEQUENCE-BINDING PROTEIN) (TBP). [SWISSPROT;Acc:P20226] 0.24860218
TBX19 0.0222862 2452 0.102768 T-BOX TRANSCRIPTION FACTOR TBX19 (T-BOX PROTEIN 19). [SWISSPROT;Acc:O60806] 0.216859334
TBX6 0.018755 2695 0.0901743 T-BOX TRANSCRIPTION FACTOR TBX6 (T-BOX PROTEIN 6). [SWISSPROT;Acc:O95947] 0.207986089
TCEA2 0.0564551 2422 0.258811 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 2 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 2) (TESTIS-SPECIFIC S-II) (TRANSCRIPTION ELONGATION FACTOR TFIIS.L). [SWISSPROT;Acc:Q15560] 0.218132537
TCIRG1 0.202198 1719 0.852079 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 3 (V- ATPASE 116-KDA ISOFORM A3) (OSTEOCLASTIC PROTON PUMP 116 KDA SUBUNIT) (OC-116 KDA) (OC116) (T-CELL IMMUNE REGULATOR 1) (T CELL IMMUNE RESPONSE CDNA7 PROTEIN) (TIRC7). [SWISSPROT;A 0.237299593
TCP1 0.063706 3099 0.673766 "T-COMPLEX PROTEIN 1, ALPHA SUBUNIT (TCP-1-ALPHA) (CCT-ALPHA). [SWISSPROT;Acc:P17987]" 0.094552115
TCP11 0.0342505 2124 0.150141 T-COMPLEX 11. [RefSeq;Acc:NM_018679] 0.228122232
TCP11L1 0.038682 2125 0.169567 0.228122217
TCP11L2 0.0476698 2123 0.208966 0.228122278
TDO2 0.157338 676 0.591312 "TRYPTOPHAN 2,3-DIOXYGENASE (EC 1.13.11.11) (TRYPTOPHAN PYRROLASE) (TRYPTOPHANASE) (TRYPTOPHAN OXYGENASE) (TRYPTAMIN 2,3-DIOXYGENASE) (TRPO). [SWISSPROT;Acc:P48775]" 0.26608288
TENC1 0.260485 759 0.987283 C1 DOMAIN-CONTAINING PHOSPHATASE AND TENSIN-LIKE PROTEIN ISOFORM 2; PUTATIVE PROTEIN TYROSINE PHOSPHATASE; C1 DOMAIN-CONTAINING PHOSPHATASE AND TENSIN-LIKE PROTEIN; TENSIN 2. [RefSeq;Acc:NM_015319] 0.263840257
TEX28P2 0.0289523 803 0.1105 TESTIS-SPECIFIC PROTEIN TEX28. [SWISSPROT;Acc:O15482] 0.262011765
TEX9 0.0403612 900 0.155595 0.259399081
TFCP2 0.209001 642 0.779209 "TRANSCRIPTION FACTOR CP2; TRANSCRIPTION FACTOR CP2, ALPHA GLOBIN. [RefSeq;Acc:NM_005653]" 0.268222005
TFCP2L1 0.198895 641 0.741531 LBP-9. [RefSeq;Acc:NM_014553] 0.268222097

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/