Matt:LabNotes/2014-3-7
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Cell Type with Most Expression of Agi26k0gap Probe Genes[edit]
- Strategy
- Get gene expression (microarray) data from GEO for each cell type
- Rank genes from high expression to low
- Sum the ranks of genes included in Agi26k0gap probeset
- The cell type with lowest sum has most expression for genes of interest
- Agi26k0gap Genes: Dec2012_0bp_gap_probes.txt and Dec2012_0bp_gap_probes_stemCellGenes.txt
PGP1f[edit]
- Sample: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM313643
- Platform: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL7182
- Used Excel VLOOKUP() to match gene name to intensity values and rank: Gene Expression Rank
Result[edit]
- ACTB Rank: 49
- RAB7A Rank: N/A
- MALAT1 Rank: 20,709
Agi26k0gap
Gene | PGP1f Rank |
ADM | 3 |
LGALS1 | 4 |
ANXA2 | 8 |
VIM | 10 |
TIMP1 | 36 |
S100A10 | 38 |
ACTB | 49 |
CXCL12 | 57 |
IFITM2 | 78 |
GNAS | 83 |
ATF4 | 114 |
CST3 | 134 |
SRPX | 159 |
ENO1 | 164 |
ANXA1 | 167 |
RTN4 | 176 |
COLEC12 | 195 |
KIAA1199 | 200 |
CCND1 | 204 |
RHOA | 207 |
SNX3 | 209 |
ACTA2 | 211 |
IGFBP4 | 212 |
SOD1 | 217 |
NPC2 | 223 |
KIAA0101 | 232 |
CCR6 | 250 |
FHL2 | 252 |
CTSK | 254 |
PDGFRA | 260 |
LOX | 264 |
CLIC1 | 265 |
ANXA5 | 267 |
PRRX1 | 273 |
GJA1 | 326 |
CLIC4 | 328 |
EFEMP1 | 337 |
THY1 | 346 |
FST | 349 |
COL3A1 | 356 |
GNG11 | 357 |
LMO4 | 359 |
FXYD5 | 360 |
APOD | 371 |
MOXD1 | 391 |
TAGLN | 403 |
GREM1 | 425 |
SCARB2 | 430 |
MMP3 | 434 |
COX8A | 435 |
NT5E | 436 |
COL6A1 | 440 |
STC1 | 441 |
KCNK2 | 452 |
IFITM1 | 453 |
LAMP1 | 469 |
HOXC6 | 471 |
CAMK2N1 | 489 |
SPARC | 491 |
LAMC1 | 527 |
GLO1 | 544 |
PTRF | 558 |
BTG1 | 572 |
GLTP | 577 |
LMNA | 597 |
CYR61 | 609 |
NNMT | 618 |
SERPINH1 | 623 |
TMEM47 | 625 |
COL5A2 | 641 |
STOM | 650 |
RND3 | 651 |
XBP1 | 655 |
CNN2 | 660 |
CA12 | 667 |
PCDH18 | 675 |
COMMD3 | 681 |
MMP1 | 695 |
SCD | 713 |
S100A11 | 733 |
SERPINE1 | 734 |
HEBP2 | 756 |
PPAP2B | 759 |
FAP | 780 |
ZDHHC9 | 783 |
MFAP5 | 792 |
COMT | 793 |
ATP2A2 | 795 |
LAMP2 | 798 |
ACTN1 | 800 |
RRBP1 | 818 |
SNAI2 | 852 |
LIPA | 868 |
KLF6 | 870 |
DDT | 883 |
PTGS2 | 890 |
CRABP2 | 901 |
AHNAK | 902 |
AEBP1 | 909 |
SH3PXD2A | 912 |
LDB2 | 916 |
TFPI2 | 918 |
PHGDH | 924 |
OAF | 932 |
MFGE8 | 936 |
TNFRSF11B | 946 |
OLFML3 | 951 |
THBS2 | 955 |
TMEM87A | 958 |
CLNS1A | 965 |
SRGN | 968 |
CCL2 | 977 |
GOLGA7 | 988 |
Agi26k0gap_Stem
Gene | PGP1f Rank |
DCN | 13 |
ITGB1 | 43 |
CD44 | 93 |
COL1A2 | 138 |
MME | 221 |
RAC1 | 353 |
COL1A1 | 418 |
ANPEP | 530 |
ILK | 551 |
DPP4 | 864 |
HDAC2 | 910 |
HDAC1 | 922 |
PDGFRB | 1000 |
NCI-H1975 Cells[edit]
- Sample: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM887393
- Plastform: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15308
MATLAB
Celstruct = affyread(GSM887393.CEL)
- Intensities only matched to probe (X,Y) coordinates
- Athurva recommended using R to read affymetrix CEL files
R
biocLite() library(affy)
- R couldn't find the affymetrix library even after reinstalling R and Bioconductor
Conclusion[edit]
- Will use Agi26k0gap probe set in PGP1f cells
- Microarray data shows the probe set contains 4 genes in the top 10 and many more in the top 100
- ACTB was ranked 49 and MALAT1 20,000+, which is near the lowest rank possible and we could still detect these
- We know good culturing conditions for PGP1f to express mRNA > rRNA
- Here are the Agi26k0gap padlock probe sequences for genes in the top 13 of PGP1f
Dye-Probe | Sequence | Probes in brain | Probes in stem | Probes in top13 Genes | Gene | ' |
dcProbe0-Cy3 | ACGTATCGGTAGTCGCAACGCA | 3641 | 0 | 1 | VIM | |
dcProbe1-Cy3 | GTCTTGCGTGCGATACGGAGTA | 2894 | 0 | 1 | LGALS1 | |
dcProbe2-Cy3 | TCTACTTCGTCGCGTCAGACCA | 2950 | 491 | 1 | VIM | |
dcProbe3-Cy3 | CCGTTTGATCGTTCGACCGAGA | 2910 | 45 | 0 | ||
dcProbe4-Cy3 | CTACCATTCGCGTGCGATTCCA | 3014 | 196 | 2 | VIM | DCN |
dcProbe0-FAM | ATGTATCGCGCTCGATTGGCAG | 4097 | 0 | 1 | LGALS1 | |
dcProbe1-FAM | CAACGGTATTCGGTCGTCATCC | 2849 | 0 | 0 | ||
dcProbe2-FAM | TAGAACTTGCGCGGATACACGG | 2925 | 293 | 2 | DCN | ADM |
dcProbe3-FAM | CGAATTGTCCGCGCTCTACGAT | 3190 | 220 | 1 | ANXA2 | |
dcProbe4-FAM | TCGGAATACGTCGTTGACTGCG | 2927 | 207 | 1 | ANXA2 |